NEW YORK — The New York City Department of Investigation raided the Queens County Sheriff’s Office on Thursday amid a probe into whether deputies improperly seized cash from unlicensed pot shops, sources said.

A source familiar with the matter told the New York Daily News that DOI agents searched the Sheriff’s Office headquarters on Starr Avenue near Borden Avenue in Long Island City as part of an ongoing investigation into the agency.

Sheriff Anthony Miranda told members of the City Council at a Sept. 17 hearing that his office does not handle cash retrieved during raids of illegal pot shops, maintaining it is the NYPD’s responsibility to voucher all seized funds.

“Since ‘(Operation) Padlock to Protect,’ the vouchering process has been designated with the NYPD,” Miranda said when asked by City Council Finance Committee Chairman Justin Brannan (D-Brooklyn) about how much revenue the sheriff’s office is expected to generate from illicit marijuana shop raids this year.

“They are the ones who voucher the property depending on the circumstances of the location,” Miranda said at the hearing. “They will either voucher it as safekeeping or voucher it as investigatory evidence depending on the different circumstances.”

But union officials refuted Miranda’s claims, saying deputy sheriffs are routinely asked to voucher cash and cannabis products.

One source told the Daily News they informed DOI that they witnessed cash being removed from shops by deputies.

It has not been alleged the sheriff’s office was skimming funds from the seized cash.

Tensions between Miranda and the union have been running high, with the union calling on Miranda to resign for creating a “hostile work environment” that’s led to an exodus of rank-and-file members.

It was not immediately clear what has happened to cash seized during the “Padlock to Protect” operations run by a city task force that includes both the sheriff’s office and the NYPD.

Miranda told Brannan during last week’s hearing he would follow up with the NYPD and supply additional information to the City Council.

Complaints over the issue have been filed with the DOI, which has begun an inquiry and interviewed witnesses, sources said. The sources also noted the cash seizures were among various issues being looked at by DOI, but specifics of other lines of inquiry weren’t immediately clear.

DOI spokeswoman Diane Struzzi declined to comment.

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