The coronavirus outbreak is putting extraordinary stress on New York City’s judicial system, forcing lengthy delays in criminal proceedings and raising growing concerns about the rights of defendants.

Since February, the backlog of pending cases in the city’s criminal courts has risen by nearly a third — to 39,200. Hundreds of jury trials in the city have been put on hold indefinitely. Arraignments, pleas and evidentiary hearings are being held by video, with little public scrutiny. Prosecutions have dropped off, too, as the authorities have tried to reduce the jail population.

Three months into the crisis, the city’s once bustling courthouses are barely recognizable. Their spacious lobbies and halls, formerly filled with people, are nearly empty, and in the courtrooms clerks in surgical masks tend to virtual hearings on giant video screens. Two centuries of face-to-face judicial traditions have either been cast aside or moved online.

The health crisis has tested the technical capacity of the courts and their ability to preserve due process in an emergency. Around the state and country, local and federal courts are dealing with similar issues, installing plastic “sneeze shields” and setting up directories of remote proceedings on YouTube.

Then in May, another shock arrived: New York City erupted into protest over the killing of George Floyd, flooding the system with hundreds of arrests. Prosecutors’ offices, which had worked for weeks with skeleton staffs, sprang back into action, and court officials doubled the number of video arraignments in Manhattan. It was, as one city judge described it, “a crisis within a crisis.”

Two weeks ago, the state courts in New York City took a first small step toward physically reopening: Judges started returning to their chambers, though they are still holding court virtually.

No one has quite figured out yet how to bring the public back safely to New York City courthouses, nor how to resume trials and state grand jury hearings. Officials said the challenge of balancing public health and the requirements of the law is likely to persist for some time.

“It’s a situation we’ve just never seen before,” said Melinda Katz, the Queens district attorney.

Trials have stopped

In spring 2019, there were about 570 criminal trials in New York’s state courts, and the city’s courthouses were among the busiest. Before the crisis, there were as many as 15 jury trials going on each day in Manhattan Criminal Court alone.

This year, all trials statewide were postponed in mid-March until further notice. To make the move legal, Gov. Andrew M. Cuomo suspended the state’s speedy trial laws.

Since then, not a single trial has been held in the city, and several mistrials were declared during trials that could not be finished. Defendants have had to wait, many of them in jail.

Chester Taylor and Darius Hastings, for instance, were nearing the end of their murder trial in March when the judge suspended the proceedings because of the pandemic.

Since then, the two men, who maintain they are innocent in the 2016 shooting of a Harlem man who died two years later, have sat in cells at the Manhattan Detention Center, trying to avoid the virus.

“I waited over two years for my day in court,” Mr. Taylor, 34, said during a telephone interview from jail. “We’re supposed to be innocent until proven guilty.”

The judge is now seeking to restart the trial on July 14, with jurors spaced out in the gallery, the defendants at separate tables and the prosecutors in the jury box, Mr. Taylor’s lawyer, Dawn Florio, said.

The halt on jury trials, while highly unusual and difficult for defendants, has not yet reached a crisis point. Even under the best conditions, it can take years for cases to move from arrest to trial, and only about 5 percent ever get that far; most end with a plea bargain.

Still, jury trials are the heart of the justice system, and state court officials face significant hurdles as they resume. “I can’t tell you we have a precise plan,” said Judge Lawrence Marks, the state’s chief administrative judge. “It will be one of the last phases.”

Unlike other court proceedings, jury trials require people to hear evidence together and then deliberate in close quarters. “The whole idea of ‘12 Angry Men’ screaming at each other over a telephone, over a Zoom network, would be ridiculous,” said one defense lawyer, Joel Cohen.

In Federal District Court in Manhattan, architects and carpenters have been redesigning courtrooms, building jury boxes with additional space and inserting plexiglass dividers to keep jurors safer. Shields are being put in front of witness stands and at lecterns where lawyers argue.

Certain precautions that are being considered may raise legal issues. “You can’t put a mask on the witnesses in a criminal trial because the defendant has the right to see them,” Chief Judge Colleen McMahon said.

“Jury trials are way, way down the road,” she added.

Some jurists warn that a prolonged delay in resuming trials could violate the Constitution.

“If well past July and for months to come, it is still dangerous for 12 people to gather together in tight quarters to hear and determine civil and criminal cases, it is not easy to see how the constitutional right to a jury trial will be genuinely met,” Judge Jed S. Rakoff wrote in The New York Review of Books.

A brave new world of virtual hearings

One Monday evening last month, Judge Paul McDonnell of Manhattan Criminal Court approached the desk in his living room that held two laptops and a bottle of hand sanitizer. He pulled a black robe over his light gray suit and tie.

“I always wear my robe,” Judge McDonnell said. “I want the defendant to understand who I am.”

For the next eight hours, the judge conducted night court for people arrested in Manhattan on charges ranging from gun possession to assault — all from his Brooklyn apartment. Like other judges in the city, he was recently ordered to return to his chambers and hold court virtually from there.

Before the pandemic, Judge McDonnell had worked in a paneled courtroom, overseeing a mass of humanity — defendants, clerks, prosecutors, defense lawyers and family members — all in close quarters, engaging in the rituals of American justice.

Courthouses in New York are still open to the public, officials say, and people have a right to enter courtrooms and view proceedings on a video monitor. Still, court officers are limiting traffic into the buildings, and the digital links needed to watch online are not being made public.

People who are arrested no longer set foot inside a physical courtroom to hear the charges against them in an arraignment. They now sit in a windowless booth in a courthouse cell, looking into a camera and speaking into a microphone on the wall.

Felony arraignments have fallen by 50 percent this spring compared to last, largely because far fewer people were arrested in the first weeks of the pandemic. That has made the transition to video somewhat easier, though not any faster. In the months after the courts moved to a virtual system, the average arrest-to-arraignment time has increased by as much as three hours.

Before the pandemic, lawyers generally did most of the talking in court. In the video hearings, defendants, no longer in the same room as their lawyers, have been more prone to sudden and sometimes incriminating outbursts.

On May 8, a man arrested in the Bronx on an assault charge became upset when a judge, sitting at home, set his bail at $5,000. Moments after being led away, the defendant ran back into the booth, ranting about details of the assault, a potential disaster for his defense. A court official asked him to step outside then muted his audio feed.

During a pause in the arraignments, a cat jumped onto the judge’s desk.

Another man asked a judge in Brooklyn federal court last month during a hearing over the telephone if he could have special protection because he was cooperating with the government against his fellow gang members. An uncomfortable silence followed. His lawyer hurriedly asked the judge to seal the transcript.

Tina Luongo, chief criminal defender for the Legal Aid Society, mentioned another challenge: The inability to see a witness’s body language and quietly confer with the defendant seriously hampers defense lawyers.

“We’ve got to figure that out,” she said. “When we’re all on one Skype link, how do I talk to my client in a confidential way?”

Before hearings begin, lawyers can meet virtually with clients in private Skype conference rooms, but the system is not foolproof.

Lara Belkin, a lawyer for Legal Aid, was in her apartment in Long Island City representing defendants at arraignments in the Bronx on a Friday last month, clicking through courtroom links on Skype looking for a client. She entered one virtual room to find another lawyer already using it with a defendant. “Oops,” she said, clicking out quickly. “That’s not good.”

After finding the correct link, she yelled the name of a newly arrested individual into an empty video booth. “Please step into Booth D,” she shouted. As they discussed the case, the audio cut in and out, and she asked the man to speak a little louder. He faced a misdemeanor charge for carrying a Taser.

Ms. Belkin needed to find out if the government was seeking to keep her client in jail until his trial. In court, she could simply have walked up to the prosecutor’s table. On this day, however, it took her more than an hour to reach the prosecutor by phone.

During night court on May 11, Judge McDonnell waited for two hours before the first defendant appeared — a 35-year-old man charged with gun possession. The light on the man’s face in the booth was bad. “It’s dehumanizing,” the judge said. “I’m asking for light.”

The serial number on the pistol the man had been found with was scratched off. But he didn’t have a long record, and the judge said the police officer’s reason for stopping him might be called into question. Yet, the judge said, sending the defendant to jail with high bail might expose him to the virus.

“It’s not easy,” Judge McDonnell said. Some jurists, he went on, think it’s not appropriate for a judge to consider whether jails are safe, but then he added, “We all weigh it.” The pandemic has also shut down many mental health programs he was once able to use as an alternative to jail.

“What am I supposed to do?” the judge said. “Prior to Covid, I had lots of tools.” He set bail terms that would have required the defendant to come up with at least $2,500. “I don’t have any money,” the defendant said, before being led away.

The new normal

Perhaps the biggest headache for the state courts has been the inability to convene grand juries, which given their size — they are usually composed of 16 to 23 people — have been unable to gather safely.

Grand juries have traditionally acted as a citizen’s check on overzealous prosecutions by scrutinizing evidence and approving formal charges. They are also used by state and federal prosecutors to conduct long-term investigations. Without them, the rights of both defendants and crime victims are less assured.

In New York, anyone arrested on a felony charge must be freed if a grand jury fails to indict within six days. Gov. Cuomo has suspended that deadline, which last month had left about 400 people in custody — in jails that have become hotbeds of infection — without the cases against them being tested. That figure dropped to 87 as of last week.

“You’ve had no opportunity to challenge the evidence,” said Elizabeth Daniel Vasquez, a lawyer with Brooklyn Defender Services.

Unable to convene grand juries, the city’s five district attorneys are turning instead to preliminary hearings, which have not been conducted in New York in decades. At the hearings, judges hear witnesses, consider evidence and decide if prosecutors’ charges are warranted. Like everything else these days, these hearings are being held by video.

Weeden Wetmore, the district attorney in upstate Chemung County, convened a remote preliminary hearing last month — on the portico of his office. The judge was at the local county courthouse, the defendant in the county jail, and the defense lawyer at his office. The witness, a 17-year-old girl who said she had been robbed at knifepoint, arrived to testify on a bicycle.

Mr. Wetmore plans to continue the al fresco hearings for as long as possible.

“We’re praying for good weather,” he said.

In Queens, Ms. Katz has set aside six rooms on three floors of her office so that simultaneous hearings can be held. Each room has its own feed: three for her prosecutors and three for their witnesses. The witnesses could not be in the same room as prosecutors to avoid suggestions that they were being coached.

“The criminal justice system is not exactly known for its flexibility,” said Jennifer Naiburg, the chief deputy prosecutor in Queens. “We’re definitely flexible now.”

The city’s two federal courts, in Manhattan and Brooklyn, have adapted more smoothly to the crisis. Under their auspices, grand jurors began meeting again recently outside the city, in White Plains and Central Islip. And in both courts, regular audio and video hearings have been held, with dial-in numbers for the public clearly posted on electronic dockets.

But obstacles remain, like how to bring in large numbers of prospective jurors for screening.

Take the capital case of the Uzbek man accused in a 2017 terrorist attack that killed eight people on a Manhattan bike path. More than 1,000 prospective jurors had come in to fill out jury-selection questionnaires, but later were dismissed after Judge Vernon S. Broderick postponed the trial indefinitely because of the pandemic. The process would have to be redone.

At a teleconference in April, a jury official explained that bringing in so many potential jurors might take three days “with things being normal.”

But, with social-distancing guidelines, she added, “I don’t know what the new normal would be.”

Shaila Dewan contributed reporting.