Three newly discovered boxes of evidence are threatening to cause a mistrial — or at least a trial delay — in the case of the former SoHo bodega clerk who has confessed to killing Etan Patz back in 1979, defense attorneys said in court Monday.

The boxes turned up last week at a police warehouse in Harlem and only portions of the casework were turned over to accused Patz killer Pedro Hernandez’s lawyers to review over the weekend as prosecutors worked to get them copies of the voluminous files.

“Given this massive disclosure at this point, there may be issues,” Alice Fontier, one of the defense attorneys, told Manhattan Supreme Court Justice Maxwell Wiley out of the presence of jurors.

“We may need to recall some of their witnesses, we may need to add people to our witness list, we may need to move for a mistrial. There’s a lot of very relevant information in here.”

She said one box alone contains nearly 1,500 pages of information ranging from police records from the decades-long investigation to handwritten notes from a detective who was probing Jose Ramos, a suspect who was never charged in the murder of the 6-year-old.

Other information includes correspondence between police and two informants who were working to link Ramos to Patz’s death.

Lead defense attorney Harvey Fishbein said it’s too early to know how the new-found evidence could affect the trial.

“At a minimum, it shows the historical file is incomplete,” he told reporters. “We’re hopeful we don’t have to ask for a mistrial.”

The trial for Hernandez, 54, accused of luring little Etan to the basement of a relative’s grocery and then killing him before dumping his body with commercial trash nearby, began in late January and could last more than two months.

On Monday, jurors watched the first recorded confession Hernandez made to three NYPD detectives — including Det. David Ramirez, who testified Monday — at the Camden County Prosecutor’s Office in New Jersey.

In the hour-long video taken on May 23, 2012, Hernandez starts to sob when recalling the creepy encounter.

“I saw him and I asked him, ‘Do you want something to drink?’” Hernandez recalled. “Then I asked him to go in the basement … We went downstairs. I was standing behind him and I put my hands around his neck.”

He then tells investigators in a soft voice that the little boy was still alive when he stuffed him in a garbage bag and dumped him in a box.

“I know when I did what I did, he was alive. He wasn’t dead. Somebody must’ve did something,” he says through tears.

One of the detectives then asks Hernandez if he had something to say to Patz’s family.

“That I’m really sorry, that I never meant to hurt their child,” he said quietly.

Throughout the video, NYPD Det. Jose Morales consoles Hernandez by putting his hand on his shoulder and rubbing his head.

“That’s strength, that’s the strength of the lord. I can’t tell you how proud I am of you,” Det. James Lamendola tells him.

The following day, Hernandez makes a similar confession in a three-hour videotaped interrogation.

Jurors also saw another video from later that evening in which Hernandez brings detectives to 113 and 115 Thompson Street, where he says he allegedly dumped Etan’s body in a basement.

Fishbein, who’s argued Hernandez has a low IQ and was psychologically coerced into confessing to the crime, blasted the video as being questionable.

“Bottom line is, both locations are wrong,” Fishbein told reporters. “What Mr. Hernandez says is unreliable.”

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