The lone firefighter who piloted an FDNY fireboat involved in a fatal accident was removed from his duties in a marine unit pending the results of a Coast Guard investigation, The Post has learned.

Officials for the first time identified Thomas J. Waller as the firefighter who helmed FDNY’s Marine 1 Bravo on a pleasure cruise for four civilians on June 17, when it collided with a private fishing boat in the East River, killing a visiting Belgian firefighter, Sgt. Johnny Beernaert.

Waller, 47, took the boat for an evening ride without adequate staffing or permission, officials said, but sources insisted he did so at the behest of an unspecified boss.

At 10:09 pm, the commercial fishing boat “Honcho” struck the fire boat, critically injuring Beernaert, 53, who later died at Bellevue Hospital.

Also aboard, Beernaerts’s wife, Heidi Vermandel – who has sued the city – retired FDNY Capt. Stephen Lonergan and his wife Elizabeth, were treated for minor injuries, as was Waller, officials said at the time.

Waller was reassigned to an administrative position shortly after the crash, said FDNY spokesman Jim Long. 

“He hasn’t been on the boat since that time. He has a desk job,” Long said.

Reached at his Long Island home, Waller would not comment.

The Uniformed Firefighters Association, the union which represents Waller, did not return messages seeking comment.

The US Coast Guard has not released any findings, saying its 9-month investigation remains ongoing.

Besides Waller, a lieutenant, captain and battalion chief – all on duty the night of the crash – were relieved of their duties and reassigned, Long said. None was suspended without pay.

FDNY commissioner Laura Kavanagh also pressured then-Acting Chief of Operations Richard Blatus, who had ultimate oversight of the marine division, to retire this month, according to a lawsuit filed by three other chiefs Kavanagh demoted in a department shakeup.

Additional reporting by Rich Calder