Attorneys for Marine Cpl. Lindsey Scott charged yesterday that a key defense witness has been intimidated and asked to take a lie detector test by the Naval Investigative Service.

The defense's complaint was the latest in its efforts to hold the NIS handling of Scott's case up to doubt and, in some cases, ridicule. In cross-examination of government witnesses during the first seven days of Scott's court-martial at Quantico Marine Corps base, the lawyers have suggested that, at best, the investigation was a bungling display of oversight and incompetence and, at worst, a ham-handed attempt to frame an innocent man.

Marine prosecutors in a number of instances have not tried to rebut that criticism, but rather to shift the focus to evidence that they say points to Scott as the man who raped the wife of a military policeman and cut her throat at Quantico five years ago.

The witness at issue yesterday, Marine Staff Sgt. Sammy Lee, did not testify in Scott's first court-martial in 1983 on charges that Scott raped, sodomized, abducted and attempted to murder the woman. Scott's attorneys said Lee had only recently emerged as a potentially important defense witness.

Lee, who worked at Quantico's photo lab in 1983, is expected to testify next week that when the woman was brought before a lineup of six marines to identify her assailant, she remarked that she couldn't identify any of them.

Scott's attorneys said yesterday that Lee has been "battered" by three recent NIS interrogations in New Orleans, where he is stationed. He is the only one of 29 defense and government witnesses who has been asked to submit to a polygraph examination in connection with this case, sources said.

Judge Eligah D. Clark refused to grant a request by Scott's attorneys that Lee be ordered immediately to Quantico so that he escapes what they described as NIS "coercion." Clark said Lee need not take a polygraph test. "Staff Sgt. Lee has a clear and immediate remedy," the judge said. "Just say no."

Investigators, both at the current proceeding and the one in 1983, have said the woman picked Scott and one other man who she said resembled her assailant out of the lineup. The woman has said in court that she was "99 percent positive" from the lineup that Scott was the man who attacked her.

The woman's identification of Scott is a key aspect of the prosecution case because there is little else to establish that Scott was the man who tricked the woman into accepting a ride in his car the night of April 20, 1983, drove her to a remote area of the base and attacked her.

Two forensics experts testified yesterday that physical evidence recovered from the victim, from Scott and from Scott's car fails to link Scott to the woman or is inconclusive.

Scott was convicted at his first court-martial and sentenced to 30 years at hard labor. After serving nearly four years of that term, his conviction was overturned last summer by the nation's highest military court, which ruled that Scott had received an ineffective defense.

The thrust of the criticism by Scott's attorneys is that the NIS investigators prematurely fixed on Scott as the assailant and failed to consider the possibility of other suspects. The lawyers suggested that the investigators gathered evidence to inculpate Scott and ignored evidence that may have exculpated him.

For example, NIS agent David C. Martin testified Monday that there were about 90 blacks in 1983 in Security Battalion at Quantico, the unit in which Scott worked as a criminal investigator. "What other black men . . . were investigated in any depth?" asked Gary R. Myers, one of Scott's attorneys.

"None that I'm aware of, sir," replied Martin.

In addition, it has come out in testimony that NIS and other agencies' investigators:Did not seize as evidence from Scott's car a cigarette butt, plastic car caddy and light bulb -- none of which were mentioned by the woman in her description of the assailant's car. Did not collect or analyze spots on the road -- which appeared to be blood -- found near where the victim was found wandering and dazed after the attack. Lost or destroyed photo negatives of Scott's car. Did not seize or obtain a search warrant for the underwear Scott was wearing the night of the attack.