By Frank G. Runyeon

Law360, New York (June 3, 2020, 11:08 PM EDT ) Public defenders in New York City filed suit on Wednesday to free hundreds of people they say were illegally detained amid days of intense protests and looting following the killing of a black man in police custody in Minnesota.

The Legal Aid Society filed a two-page writ of habeas corpus with scant detail demanding the release of anyone who has been jailed for over 24 hours without a warrant or arraignment in violation of the New York state constitution, arguing in public statements that the "illegal" detentions are retaliation for the tumultuous street demonstrations against police brutality.

Public defenders accused the government of punishing protesters after days of clashes with NYPD officers by purposely slow-rolling their release.

Court officials told Law360 that around noon Wednesday about 300 people — triple the number reported on Tuesday evening — had been in custody in Manhattan more than 24 hours. The NYPD told Law360 on Wednesday that it has made over 2,000 protest-related arrests in the past week.

"This flagrant violation of law by the New York City Police Department appears to be designed to retaliate against New Yorkers protesting police brutality," said Tina Luongo, attorney-in-charge of the criminal defense practice at The Legal Aid Society.

Under new state bail reforms, Luongo said, "the overwhelming majority of these charges require that people be released on their own recognizance to fight their cases later in court. Instead, these New Yorkers are now being held illegally, deprived of due process and needlessly subjected to increased risk of contracting COVID-19, endangering each of them as well as the entire community," Luongo said.

"We demand the release of these people at once," Luongo concluded.

State court spokesman Lucian Chalfen told Law360 on Wednesday that the bottleneck was with the police department, not the courts.

"We are waiting for the paperwork from the police through the district attorney and it has just been slower than we are generally accustomed to," Chalfen said.

The city's Law Department, which is representing the NYPD in the lawsuit, slammed the allegations.

"The accusation that officers are retaliating against New Yorkers who are protesting is disingenuous, exceptionally unfair, and perhaps deliberately ignoring the fact that the Police Department is dealing with a crisis within a crisis," said special federal litigation chief Patricia Miller in a statement to Law360.

"The NYPD, as well as the entire criminal court system, is working within the confines of a pandemic and is now suddenly called upon not only to secure orderly protesting, but also to address rioters who are committing burglaries, destroying private property, and assaulting fellow New Yorkers. We will respond in court," Miller added.

On Wednesday morning, trial court Justice Neil Ross tried to help clear the backlog of adult arraignments between 9 a.m. and noon, all of which were handled "virtually" over a Skype for Business videoconference. In similar fashion to the first such remote arraignment in March, a video console was set up in the physical courtroom for observers and other court staff. And while the console displayed the streaming video of the remote parties, the screen  faced the empty bench and was not visible from the gallery.

"How many have we done so far?" the disembodied voice of Justice Ross asked no one in particular during a noontime break. A court officer checked her records and then walked around to the front of the screen.

"Sixteen," she responded.

"That is insane," the judge replied. "How many are in the system overall?"

The clerk told the judge she didn't know, but at the time there were nearly 400, a court clerk later told Law360.

At 12:30 p.m. Wednesday, 379 people were still in custody awaiting arraignment, 295 of whom had been jailed for over 24 hours, according to the Manhattan criminal court clerk's office and state court officials.

At that time, it was "slow going" with the arraignments of minors, a clerk overseeing arraignments told Law360, noting that the court had done about a dozen, but hoped to release the remainder of the minors in custody by lunch time.

The clerk overseeing arraignments hoped to complete 70 arraignments in Manhattan by the end of the business day.

By late afternoon, a state court official said the system planned to keep the arraignments going all night long, "as long as the paperwork keeps flowing."

"We're remaining open for whenever the paperwork comes down the pipeline from police," Chalfen said.

By 6:30 p.m. Wednesday, Legal Aid told Law360 the number of New Yorkers illegally jailed more than 24 hours in Manhattan had decreased by 50 to 241. The citywide total, however, was 300.

During one 30-minute stretch in back-to-back arraignments, Justice Ross released six defendants who were all accused of looting during the protests, a charge rendered as burglary in the third degree. Depending on the case, the defendants also faced a variety of different charges that painted a dire portrait of the past week's events: petit larceny, criminal possession of stolen property, inciting a riot.

Justice Ross pointedly noted for the defendants with criminal records that the new bail reform law stopped him from setting bail that might have kept them in jail. The judge released the alleged looters.

Authorities have taken pains to separate the protesters from the looters, but the allegation that the police are denying peaceful protesters their civil rights has struck a nerve in the wake of the death of George Floyd in Minneapolis. On Wednesday, Minnesota prosecutors upgraded the charges against Derek Chauvin, the officer they say killed Floyd by kneeling on his neck, to second-degree murder.

New York police have said they will investigate social media videos and photos that show officers striking protesters and journalists with billy clubs and violently arresting people in the street, but both the state attorney general as well as the Brooklyn and Manhattan district attorneys have vowed to independently investigate police misconduct, asking the public on Twitter for investigative leads.

The state attorney general and DA's offices declined to provide the specific number of complaints of police misconduct against protesters, but a spokeswoman for the Manhattan DA said it had received "several." The state attorney general's Twitter account had responded to over two dozen online reports with requests for further details.

The governor and state legislative leaders have also said they are considering repealing or reforming a law that shields records of police misconduct from public disclosure.

The detainees are represented by Corey Stoughton, Steven Wasserman, Russell Novack, Marlen S. Bodden and Emma Goodman of The Legal Aid Society.

The NYPD is represented by the New York City Law Department.

The case is People of The State of New York ex rel. Corey Stoughton on Behalf of Lazeme Harris et al. v. Dermot Shea, Commissioner, New York City Police Department or anyone having custody of petitioners, index number 100446/2020, in the Supreme Court of the State of New York, County of New York.

--Additional reporting by Emma Whitford. Editing by Michael Watanabe.

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