A federal prosecutor, accused last week of altering documents in a tax conspiracy case here, also was accused of intentionally withholding a key document from the defense attorney -- while giving it to the jury -- in another federal case in Alexandria five years ago.

The trial judge threw out a conviction in the Alexandria case and ordered a new trial after the accusations by the defense attorney, according to court papers, and the government ultimately dropped the case. The controversy arose after the defense attorney reported that a document given to the jury to study showed the defendant's client's signature embossed on a carbon copy, but the defense's Xerox copy did not show the signature.

The allegations of misconduct -- unusual in federal prosecutions -- revolve around Assistant U.S. Attorney Elizabeth H. Trimble, a veteran of the 35-member U.S. attorney's office here.

Last week, attorneys for Omni International Corp., a Rockville-based jet airplane trading company indicted on tax fraud charges, accused Trimble and at least three Internal Revenue Service agents in court papers of altering and fabricating documents and then lying about it to prevent dismissal of the case.

Trimble and her boss, U.S. Attorney J. Frederick Motz, denied the allegations but declined to discuss details, saying they will file a full response with the court later this month.

Known as a tough prosecutor among her colleagues, Trimble was attending a Justice Department conference in Boston this week. She did not respond to telephone messages left by a reporter at her hotel in regard to the allegations in the Alexandria case.

Motz, who is expected to be nominated soon by President Reagan for a federal judgeship here, again defended Trimble. In a formal statement, he said, "It is unfair to attack the reputation of a highly regarded government lawyer by publishing an article based upon a five-year-old allegation, which was at the time determined to be baseless."

This was an apparent reference to the fact that the Justice Department's Office of Professional Responsibility, an agency that investigates allegations of misconduct by department employes, took no action in the matter.

In the Alexandria case, according to court papers, U.S. District Chief Judge John A. MacKenzie ordered a new trial for the businessman, William Chappelear, charged with conspiracy and aiding and abetting bribery, after finding that Chappelear "was denied a meaningful opportunity to confront an incriminating signature" on a document given to the jury by Trimble but not to defense attorneys during the trial.

Prosecutors and defense attorneys negotiated a disposition of criminal charges against Chappelear and his business in the case. A source said the Office of Professional Responsibility decided not to investigate the allegations against Trimble after officials in the U.S. attorney's office in Baltimore indicated that the defense attorney did not consider her actions intentional. In the earlier hearing, however, the defense lawyer repeatedly called it intentional.

Trimble had been assigned to prosecute a series of widely publicized bribery and corruption cases involving the government's General Services Administration and various corporations and individuals doing business with GSA. She and fellow government attorneys had successfully prosecuted more than 65 cases, winning scores of convictions and guilty pleas from 1978 to early 1980.

In the Chappelear case, Trimble attempted to show that Chappelear participated in a scheme to give $1,017 in free CB radios and other equipment to GSA officials in exchange for more GSA business for his office supply company. Chappelear was convicted on April 2, 1980. Afterward, his attorney, Robert Bennett, filed a motion for new trial, alleging that Trimble had withheld a vital incriminating document from him, making it impossible to formulate a defense against it.

Bennett contended Trimble's action was "intentional," that it was part of a "game plan by the government to try the case precisely this way" and was a "very serious abuse of the prosecutorial power."

Judge MacKenzie, after conducting a hearing on the issue, agreed that Trimble's actions had denied Chappelear an opportunity to confront the incriminating evidence and ordered a new trial. His ruling did not address the question of whether Trimble's action was intentional.

Among the documents Trimble used, according to Judge MacKenzie's findings, were a check for $1,017 signed by Chappelear and a purchase order form for the CB radios and equipment. During the trial Trimble made "no special effort to link Chappelear to the purchase order form," the judge wrote.

For the trial, MacKenzie noted, Trimble had given both the jury and Chappelear's attorneys a set of documents used as evidence, called an exhibit book, that she said were "copies of every paper to be found in the original exhibits," including the check and purchase order form.

As is customary, the jury was given the originals, rather than copies. In her final argument to the jury, MacKenzie said, Trimble drew attention to the original of the purchase order form, noting that it contained "carbon multiple copies" and that at least one of the carbon copies bore an impression of Chappelear's signature. The implication, Judge MacKenzie said, was that Chappelear had signed the check inadvertently while it lay "immediately atop the purchase order form," thus linking him more closely to the bribe attempt.

The top sheet of the purchase order form did not bear a signature impression since there was no carbon paper between it and the check. But Trimble had provided the defense only with copies of the top sheet, not the underlying carbon copies, MacKenzie said.

"At no time prior to the final stages of closing argument," he said, "did Trimble ever refer to the original" of the purchase order form "to demonstrate that Chappelear must have known about the purchase order when he signed the check. To the contrary, the government appeared to treat the copy" given to the defense "as the faithful reproduction of the original."

During MacKenzie's hearing in the summer of 1980, according to a transcript of the proceeding, Trimble was questioned closely by defense attorney Bennett about whether she knew the defense copy of the purchase order form did not include the underlying carbons.

At one point, MacKenzie intervened. "I will ask the question," he said, according to the transcript. "Did you know, Ms. Trimble, that the succeeding pages of the original of the purchase order form bore the signature of Mr. Chappelear but that the page that was included in the exhibit book . . . did not?

Trimble answered: "I knew only the front page had been Xeroxed and put in the [exhibit] book."

MacKenzie: "You are not answering my question, young lady. Did you know that the succeeding pages following the lead page of the original did contain an impression signature of Mr. Chappelear that was not on the original page that was included in the exhibit book?"

Trimble: "Yes, your honor, I was familiar with the exhibit." Later, in response to Bennett's questions, she added, "It didn't occur to me at that point it was of any significance, but the first page of the exhibit was all that was Xeroxed for the book."

The prosecution contended that Bennett's complaint was baseless since Trimble's office had allowed defense attorneys to examine the original documents prior to trial. Bennett countered that this was overshadowed by the fact that Trimble's office had prepared the book of documents for the defense and the jury with the assurance that they contained copies of "all" documents and thus should have contained the carbons.