A raid on the home of the Big Apple’s interim police commissioner has raised eyebrows – coming just days after he took the job and as investigations swirl around Adams administration officials, The Post has learned.

Interim commissioner Thomas Donlon said in a Saturday night statement that federal authorities had taken from him “materials that came into my possession 20 years ago and are unrelated to my work with the New York City Police Department” — one week after his predecessor stepped down over a seemingly unrelated raid.

Sources told The Post that agents had been searching for classified documents Donlon may have brought home during his years with the FBI and the Department of Homeland Security — but that explanation has left a lot of law enforcement officers scratching their heads.

“The same federal agencies that ‘recommended’ Donlon to Adams also executed the warrant — less than a week after Donlon’s appointment — to search his house for 20-year-old documents,” one source said, adding that Southern District of New York head Damian Williams actually backed Mayor Eric Adams’ commish choice before he announced it.

“I can hear the agents laughing while they’re torturing the mayor,” the source continued. “It’s open season on Adams at the SDNY and FBI.”

The same source said Donlon “clearly pissed off the wrong people at the FBI,” which led the investigators to throw “another grenade in Adams’ lap and pull the [pin].”

“Donlon was collateral damage,” the source said.

Adams tapped Donlon, an NYPD outsider, to take over as the city’s interim commissioner on Sept. 12 — the same day former commissioner Edward Caban abruptly resigned because of a federal investigation that has focused on him, his brother and several other close allies and top lieutenants of the embattled mayor.

Federal agents had seized Caban’s electronic devices as part of what sources say is a sweeping corruption probe into potential influence peddling — an inquiry that’s also ensnared Deputy Mayor for Public Safety Phil Banks, Schools Chancellor David Banks and their brother Terence Banks, as well as former NYPD official Tim Pearson and First Deputy Mayor Sheena Wright.

None have been accused of crimes and it’s still not clear if the investigations are connected to one another.

Donlon — who had been running a private security company following his retirement from federal service — was yanked back into the public eye by his appointment as New York’s top cop.

On Sunday, Donlon ignored The Post as he walked out of his Upper East Side apartment — and refused to answer questions about the raid.

Some sources said the raid on his place was the feds’ way of telling Adams that nobody in his orbit is safe.

But others claimed it was just the result of a vetting process for renewed clearances — criminality had nothing to do with it.

Not everyone believed that though.

“They don’t search your house when they do security clearance,” said Joseph Pistone, the legendary FBI agent known as “Donnie Brasco” who infiltrated the Mafia in the 1970s and 1980s.

“If I were doing a background ingestion on Tom, I’d say he’s straightforward and loves his country,” said Pistone, who’s known Donlon since 1974.

“I’m flabbergasted. He’s been out of the bureau for 15 years, and look at all the positions he’s had,” he continued. “I don’t have enough good things to say about the guy.

“And now he gets appointed police commissioner, and a week later he gets his house searched,” he said. “I have no idea why they would do a search at his house. It’s nuts.”

Mark Carroll, a former assistant US attorney and retired FBI agent, echoed Pistone’s words when he called Donlon an “upstanding member of the law enforcement community, and as principled a person as they come.”

“That makes no sense,” Carroll said of the raid. “I had the highest level of clearance. I have no good way to explain it.

“It would absolutely shock me if he did anything wrong.”