Two FBI agents were removed from their posts yesterday after wiretaps on their phones -- including one at FBI headquarters -- allegedly uncovered evidence of corruption, including conversations in which the agents describe how they teamed up with a theft ring that they once supposely investigated.

An affidavit filed late yesterday in Kansas City also outlines charges that the two men stole funds budgeted for informants, then orchestrated a coverup of the thefts.

FBI Director William H. Webster said yesterday he dismissed Alan H. Rotton, a supervisor in headquarters here, and put Stephen S. Travis of the Kansas City field office on leave after tracing allegations of criminal misconduct since June. He said that such since june. He said that such charges of corruption against FBI agents are "islolated and uncommon."

Travis reportedly was not fired immediately because he is a military veteran and has appeal rights.

A federal grand jury in Kansas City has been hearing evicence about possible conspiracy to defraud the United States, theft from interstate commerce and obstruction of a criminal investigation, according to the affidavit.

In a telephone interview last night Rotton denied the charges outlined in the affidavit. He said that the quotations in the wiretapped conversations were "taken out of context" and that he never profited from the theft ring or took money intended for informatants.

Travis could not be reached for comment.

The corruption investigation of Rotton and Travis is the first involving FBI agents to surface since it was charged late last year that an agent in New York, Joseph Stabile, lied about taking a $10,000 bribe from an organized crime figure. Stabile pleaded quilty and was sentenced to prison.

Michael E. Shaheen Jr., whose Office of Professional Responsibility at the Justice Department coordinated the investigation, said yesterday that he couldn't comment on the case except to say: "The FBI's participation has been a monument to investigative excellence. No stone was left unturned. hEvery head was pursued."

The investigation of Rotton and Travis is especially startling because of the use of court-authorized wiretaps against the agents. The taps were first ordered two months ago.

A source familiar with the case said Rotton and Travis apparently never thought that the FBI would wiretap colleagues.

Rotton said last night that he never thought about being wiretapped because he didn't think the FBI would have the "probable cause" such a court order requires.

The 31-page affidavit by FBI agent Gary W. Hart in Kansas City includes excerpts from several phone calls in which Rotton and Travis discuss how to control the investigation they knew was being conducted into their activaties.

In a Sept. 25 call Rotton said that if one informant was subpoenaed before the grand jury they could have her lawyer file a motion "that they don't want to appear and do not want their identity revealed."

"Because of being certified informants for the Federal Bureau of Investigation," Travis is quoted as having replied.

"That's right," Rotton continued. "That promises were made to them that they, their identify would never be. . . revealed."

Later in the same call Rotton suggested that Travis might have to "orchestrate the [informant's] testimony a little bit."

The investigation grew out of an earlier inquiry into reported thefts from railroads in the Kansas City area.According to the affidavit, an informant in that case told other FBI agents that he had not furnished Rotton, then stationed in Kansas City, or Travis with information, nor had he been paid by them, as bureau files indicated.

Other informants used by the two agents then were questioned and also denied getting recorded payments. The affidavit said there were indications that payments of thousands of dollars in cash were made to "informants" who never existed.

There have long been rumors that some FBI agents made up informants and kept the money supposedly paid to them, but this appears to be the first evidence of such a scheme alleged in court papers.

The affidavit also contains transcripts of calls where Rotton and Travis allegedly discuss their ongoing participation in a theft ring with a "partner," Robert J. (Joe) Martain. Martain's phone also was tapped.

On Sept. 6, for instance, Martin allegedly called Rotton at his Arlington, Va., apartment and they discussed a load of refrigerators Martin had obtained. Rotton asked if Martin had "held on to any," and when told no, allegedly replied, "Well, if you hit that place again and find a freezer keep me in mind."

On Sept. 17, Travis warned Martin to avoid disposing of the stolen property in undercover fencing operations operated by law enforcement authorities in the area.

On Sept 9, according to the affidavit, Rotton and Travis talked about a new plan to steal heavy equipment.

"And they want to handle $90,000 to $100,000 worth of equipment for half, Rotton is quoted as saying.

Rotton said he might have made such comments, but they were either voiced in a light-hearted way or were made to Martin as warnings he would give to any informant.

FBI policy forbids infornants from participating in crimes. Rotton said, "The policy is one thing. The practice is another. Any informant the bureau's got is involved in illegal activity. How else are you going to get the information?

The investigation in Kansas City is being directed by Michael A. Defeo, head of the organized crime strike force there.

The affidavit shows that a team of FBI agents in Kansas City was involved in surveillance as Martin allegedly carried out thefts from boxcars at a railroad junction near Eve, Mo.

At one point in the phone call excerpts, Rotton and Travis chuckle about how Martin manages to occupy a rail detective's attention while his gang breaks into the boxcars. "He's sitting on the railroad dick while the rest of them carry the railroad off," Rotton is quoted saying with a laugh.

At another time, Martin said he would be driving east with a truckload of merchandise that he had set aside for Rotton, according to the affidavit. Rotton said he'd reimburse Martin for the cost of the trip.