The MTA has dumped the infamous CityTime contractor, cutting it out of a plan to overhaul the subway system’s radio equipment.

Top brass said they were no longer comfortable with SAIC because state Comptroller Thomas DiNapoli put a stop on the contract and said he needed questions answered.

But consultants linked to the company are currently embroiled in a criminal probe, and the MTA said that because of that, they weren’t sure when they could answer DiNapoli’s questions.

Now the agency will rebid the contract.