Asked if Gov. Pataki, who oversees the MTA, had full confidence in Louis Anemone - a former NYPD chief who was hired after the terror attacks to protect the sprawling transit system - spokeswoman Molly Fullington declined comment.

Anemone's "status within the agency has been part of a number of discussions" since the allegations were leveled, an MTA source said.

The tough words came a day after Anemone's deputy Nicholas Casale told the Daily News that MTA officials attempted to thwart a probe into agency contractors that uncovered evidence of bid-rigging, racketeering and payoffs.

Anemone made similar allegations in The New York Times.

MTA officials called the charges baseless, and said two employees recently were fired as a result of the investigation.

Anemone and Casale, who also was his deputy at the NYPD, made the accusations amid friction between them and MTA officials. Contributing to tensions are Anemone's uneasy dealings with the MTA police union over work-rule changes, sources said.

A secretive anti-terrorism task force headed by Casale was recently gutted by the MTA, and many of its members were returned to routine patrol.

The MTA inspector general is auditing the Joint Infrastructure Task Force's books, including the award of contracts to two companies staffed by former NYPD members that have shared $1.3million for providing bomb-sniffing dogs.

Casale, who is on medical leave from the MTA, also has been questioned by the inspector general about the source of a corruption allegation he made in a separate case involving former Long Island Rail Road President Kenneth Bauer. Casale has refused to disclose the name of the person, sources say.

Yesterday, Casale again called on the MTA to bolster the task force. "It would be reckless for the authority not to immediately restaff the task force with trained and dedicated personnel," Casale said.

Assemblyman Richard Brodsky (D-Westchester) said the Corporations, Authorities and Commissions Committee would hold hearings on the allegations.

"This controversy needs to be settled, not just because of the allegations of wrongdoing, but because it might cripple security operations in the MTA," he said.

Anemone did not return phone calls.