WASHINGTON - Following fresh allegations of partisan bias in the Justice Department, Sen. Arlen Specter (R., Pa.) said yesterday that the department was "dysfunctional" and would be better off without embattled Attorney General Alberto R. Gonzales at its helm.

Specter said it was President Bush's prerogative to fire Gonzales and refused to call for the attorney general's ouster. But the ranking Republican on the Judiciary Committee said there was a "likelihood" that Bush would act once the clamor from Congress abated.

"I think there's a distinct possibility, maybe probability, that the president will act on his own," Specter said in an interview. "I think the president is more likely to fire him if he's not being told what to do . . . if he didn't have the 'anvil chorus' coming down all around him and making it appear like he's yielding to pressure."

On Wednesday, the Justice Department announced that it was investigating whether Monica Goodling, former senior adviser to Gonzales, tried to determine the political affiliation of job applicants before they were hired as prosecutors.

Such a determination may violate federal civil-service laws.

The inquiry is part of a much wider-ranging probe by the House and Senate Judiciary Committees of the circumstances relating to last year's dismissals of eight U.S. attorneys.

Two of the dismissed attorneys, Paul Charlton of Phoenix and John McKay of Seattle, released statements Wednesday saying they were threatened by Deputy Attorney General Paul McNulty's chief of staff before Gonzales testified in the Senate in January.

Charlton and McKay said that the chief of staff, Michael Elston, suggested that Gonzales would not discuss their dismissals in his testimony if the two men did not publicly speak about their firings.

Specter said he was concerned with these allegations.

"That's dead wrong to try to silence these people from testifying and to issue a threat that if they do, there will be retaliation in Gonzales' testimony," the senator said. "That's intimidation."

Specter said he was also troubled with reports that Goodling used political affiliation in hiring decisions.

"I want to take a look at what the Hatch Act says and what the civil-service requirements are," he said, referring to the federal statute that circumscribes political activity by federal employees.

In the ongoing investigations of why the prosecutors were fired and what role, if any, the White House played in the dismissals, it has been disclosed that Gonzales delegated to Goodling and D. Kyle Sampson, his former chief of staff, the hiring and firing of political appointees and senior executives who did not require Senate confirmation.

Specter said he was "infuriated" by this revelation, particularly since the attorney general has professed little, if any, knowledge about the dismissals.

"I'm really angry about it. Outlandish," Specter said. "That guy would testify that he didn't know what was going on and he signed a written delegation of authority," he said of Gonzales. "I have grave questions about whether the attorney general can delegate that authority."

Despite all the accumulating accusations of political bias in the Gonzales-run Justice Department, Specter tiptoed up to the waterline of demanding the attorney general's ouster but would not plunge in.

"The decision on whether to fire him or not is the president's," Specter said. "I'm not going to tell the president how to run the executive branch."

Carl Tobias, a constitutional authority at the University of Richmond Law School and an avid Specter-watcher, said the senator's position was not surprising, given the lack of cooperation by the Justice Department and the White House to provide "sufficient information" about what really happened.

"Specter may also be exhibiting a healthy respect for the separation of powers and presidential prerogatives about the selection of cabinet members," Tobias said.

Specter said that he had given the president "all the facts" he knew about the case, as well as some advice, but he would not disclose what was said.

Judiciary Committee Chairman Patrick J. Leahy (D., Vt.) and Specter are drafting a letter to the Justice Department asking about the nature of the ongoing investigations and whether the U.S. attorneys were asked to resign because they were pursuing matters that headquarters didn't want them to pursue.

"It's a ticklish question to ask because of the confidentiality of those investigations," Specter said. "Now there's sufficient grounds to pursue this. . . . It's not just fishing. It has the potential to be a real blow-up."

In another matter that arose during the interview, conducted in Specter's office, the senator said he had met yesterday with local residents who oppose Pennsylvania's plan to redevelop the Willow Grove Naval Air Station.

Last week, the Navy scotched a plan by which the state would lease the land once the base closed and turn it into a combination military facility and civilian emergency-preparedness center.

The local group, Horsham Land Reuse Authority, told Specter it had been rebuffed in its efforts to talk with state officials.

"I told them I would help them get a meeting," Specter said. "They don't like the governor's plan. They think the decision ought to be made by the local planning people."

Specter also said he had consulted with Rep. John P. Murtha (D., Pa.), head of the Defense Appropriations panel, about crafting legislation to override the Navy's objections.

"We're giving it strong consideration," Specter said.

Contact staff writer Steve Goldstein

at 202-408-2758 or slgoldstein@phillynews.com.