The Manhattan district attorney’s office is investigating overtime sex allegations against the NYPD’s top uniformed cop, a spokesman said Saturday.

The investigation into now-former department head Jeffrey Maddrey was launched after the Post uncovered explosive allegations from a subordinate who claimed Maddrey had sex with her in exchange for massive overtime.

Maddrey resigned Friday evening after The Post contacted Lt. Quathisha Epps had inquired.

“These are extremely serious and disturbing allegations that allegedly occurred at NYPD headquarters in Manhattan,” said District Attorney spokesman Alvin Bragg. “We’re investigating.”

Epps told The Post in an exclusive interview that Maddrey would have sex with her in his office on the 13th floor of One Police Plaza.

Maddrey proposed to her after she revealed she was in financial distress, Epps claimed in a tear-filled interview.

“He demanded ‘anal sex, vaginal sex, oral sex.’ He always asked me to kiss his penis,” she claimed.

Maddrey, who denied the allegations, immediately resigned after questions from The Post.

Mayor Adams called the allegations “extremely concerning and alarming,” and the NYPD promised its own investigation.

Epps recently made headlines for emerging as the NYPD’s highest-paid employee while working an administrative job in Maddrey’s office. Last year, she earned more than $400,000, including about $200,000 in overtime, pay stubs show.