The Port Authority’s main security contractor suffered another embarrassment yesterday when cops busted a company employee put to work in a sensitive security post, despite outstanding domestic-violence charges, The Post has learned.

Henry Marte-Batista, 27, was fired by security contractor FJC, acknowledging that background checks had failed to turn up his crimes before he was assigned to do security surveillance at the PA’s Hudson River command center in Jersey City.

New Jersey records show Marte-Batista was charged with assault in March 2009 after an alcohol-fueled incident ending with his allegedly throwing beer bottles at his wife, hitting her in the breast. PA records said he had not appeared in court to answer the charge.

This misstep adds to FJC’s long list of security foul-ups, including last month’s arrest of Peter “Bimbo” Oyewole, who used the ID of a homicide victim to land a sensitive job at Newark Airport.