Brooklyn federal prosecutors are scrutinizing Jared Kushner’s family business over official paperwork that falsely claimed the real-estate company didn’t have any rent-regulated tenants living in its New York City buildings, according to a report Thursday.

The Kushner Cos. — formerly run by President Trump’s son-in-law and adviser — was slapped with a subpoena for records in mid-March, shortly after The Associated Press revealed that hundreds of its tenants had leases subject to limits on their yearly rent hikes, according to the Wall Street Journal.

Claiming otherwise helped the company avoid strict oversight of renovations that the AP said pushed rent-regulated tenants out of three Queens buildings the company bought in 2015.

The tenants who replaced them paid higher rents, helping the Kushner Cos. sell the buildings for $60 million last year — nearly 50 percent more than what it paid, the AP said.

At the time, the company told the AP that outside companies filed the paperwork, adding that “if mistakes or violations are identified, corrective action is taken immediately.”

On Thursday, a company spokeswoman said it “has nothing to hide and is cooperating fully with all legitimate requests for information, including this subpoena.”

“We believe that this subpoena, which has already been complied with, was issued based solely on an article that appeared in the press the day before it was issued,” the spokeswoman added.

A spokesman for the Brooklyn US Attorney’s office wouldn’t confirm “the existence of any subpoena or investigation.”

Revelation of the subpoena came amid investigations into the filings by the state Attorney General’s Office and the City Council.

Brooklyn federal prosecutors are also reviewing the Kushner Cos. use of a federal investment-for-visas program — known as “EB-5” — and a $285 million loan it got from Deutsche Bank one month before the 2016 presidential election, the Journal has previously reported.