In an emotional five-page letter, a Justice Department official in Texas has warned Attorney General Janet Reno that she has been misled by people within her own department about the Waco siege and the role of federal agents.

The letter from U.S. Assistant Attorney William Johnston reveals a catalogue of frustrations--with the FBI for altering the original crime scene, with Justice Department officials for their poor handling of the 1995 congressional probes, and with the department's torts branch for trying to keep evidence from the public.

"I have formed the belief that facts may have been kept from you--and quite possibly are being kept from you even now, by components of the Department," Johnston wrote in a letter dated Aug. 30.

Justice Department spokesman Myron Marlin declined to discuss whether Reno felt she had been misled but said, "The attorney general has asked Senator Danforth to look into this matter and, we hope, find the answers."

Johnston is chief of the Waco Division in the Western District of Texas and one of the attorneys who prosecuted 11 Branch Davidians for their role in the deaths of four Bureau of Alcohol, Tobacco and Firearms (ATF) agents during the botched raid of Feb. 28, 1993. Johnston sent his letter following recent news reports that show the FBI used potentially incendiary devices during the siege of the compound 50 days later that left about 75 Branch Davidians dead.

The letter was released yesterday by the Texas Department of Public Safety as an appendix to a Texas Rangers' report outlining overlooked Waco evidence. The report raises questions about whether the FBI used gunfire on the final day of the siege, which the bureau has denied.

"There has been no information developed to date that changes the bureau's position, as stated since 1993, that no shots were fired by FBI personnel during the standoff at Waco," FBI spokesman Tron Brekke said yesterday. ATF officals suggested yesterday that any casings found in the compound could have been from shots fired by their agents on the day of the Feb. 28 raid.

The Rangers have been the primary custodians of the evidence since 1993 and have examined 24,000 pounds of items retrieved from the scene. They found shell casings "which may show that the FBI snipers fired rounds on 04-19-93," according to their report. The Rangers also found a device called a "thumper round" and concluded it was designed to knock down a door and could, under certain conditions, start a fire.

In his letter to Reno, Johnston begins with criticism of the FBI. "The FBI altered the crime scene by using armored vehicles to push Davidian vehicles away from the compound," making the Rangers' original 1993 investigation "more difficult."

Johnston wrote Reno about these problems in 1993, and since then, despite helping to win the conviction of eight Davidians, he wrote, "I have been seen by many as a mutineer."

Johnston also complained to Reno of poor treatment when he came to testify before Congress in 1995. "I was not assisted by anyone with DOJ in any real way in preparing for my testimony," he wrote. "In fact, I was handled as if I had some strain of intellectual leprosy."

In passages that take up the majority of the letter, Johnston said many people inside the Justice Department knew this past summer of the FBI's use of devices that could have caused the fire but failed to tell Reno.

"As early suspicions of these problems made their way to the media via the DPS chairman Jim Francis, I was astounded to see the Department's response was that this was 'more nonsense.' My surprise was based upon the fact that I had been updating my U.S. Attorney for weeks about this evidence," Johnston wrote. "I am in disbelief that someone in the Department did not advise you of these developments."

Johnston wrote to Reno of tensions with Marie Hagen, an attorney in the Justice Department's Torts Branch, who is defending the government in a still-pending wrongful death lawsuit filed in 1995 by the Branch Davidian survivors. Hagen "was extremely upset" with Johnston for allowing Mike McNulty, a filmmaker, to view the evidence this year.

Johnston said that much evidence already was public at the criminal trial and that "to stonewall McNulty tended to lend some credence to his already held belief that the government had something to hide." But Hagen was concerned that McNulty would supply the plaintiffs with evidence and documents they were not entitled to see. In a call to Johnston's home in June, "she ended the conversation unquenched in her anger," Johnston told Reno.

"It is my own hypothesis that the Torts Branch has had these documents for years, and that they decided not to make them available to plaintiffs," Johnston wrote. "The Torts Branch or some other component also apparently decided not to let you know about these documents."

Meanwhile, Rep. Henry A. Waxman (D-Calif.) accused Rep. Dan Burton (R-Ind.) of acting irresponsibly by calling for Reno's resignation. Waxman said it was ludicrous for Burton to accuse Reno of being involved in a coverup because the House Government Reform Committee, which Burton chairs, has had Justice Department documents since 1995 showing that the FBI used devices that could cause a fire.

"Before people make accusations about anybody, they ought to know what they have in their own files," Waxman said.

Waxman, the ranking Democrat on the Government Reform Committee, said the discovery of the documents undermines the "credibility" of Republican attacks on Reno. Waxman attached the documents to a letter he sent yesterday to former Missouri senator John C. Danforth, whom Reno appointed special counsel on Waco last week.

Waxman speculated that the attorney general simply was unaware of all the documents that her giant department turned over to Congress. Reno, for her part, has been forced to retract statements she made to Congress claiming that no devices were used that could have started the fire.

Mark Corallo, a committee spokesman, dismissed Waxman's remarks as a politically motivated attack on Republicans. He said Justice "dumped" more than 100,000 pages of documents on the committee on the eve of the Waco hearings, making it impossible to review all of them.

Staff writer Richard Leiby contributed to this report.

CAPTION: Johnston

CAPTION: Rep. Henry A. Waxman, left, released papers showing Congress had in 1995 evidence of use of possibly incendiary devices at Waco.