Ray wrote in his final report released Wednesday, just three weeks before election day, that the evidence established beyond a reasonable doubt that, contrary to her testimony, the first lady played a role in the 1993 firings of seven White House travel office workers.
The prosecutor said he decided not to bring criminal charges against the first lady, because she may not have understood her conversations with White House aides back in 1993 were interpreted as an impetus to fire the workers.
Mrs. Clinton flatly denies having a role in the firings, carried out in 1993 by then-White House administration chief David Watkins. The move prompted one of the earliest controversies of her husband's presidency - and a criminal investigation.
"The independent counsel concludes that Mrs. Clinton's sworn testimony that she had no input into Watkins' decision or role in the travel office firings is factually inaccurate," the prosecutor wrote.
The report's release, just three weeks before voters in New York decide whether to elect Mrs. Clinton to the U.S. Senate, contained few surprises because Ray had announced there would be no criminal charges. But it could give Republicans fresh fodder to attack the first lady's credibility.
Mrs. Clinton's lawyer, David Kendall, objected to Ray's conclusion as "highly unfair and misleading."
"The suggestion that Mrs. Clinton's testimony was 'factually inaccurate' as to her role in this matter is contradicted by the final report itself, which recognizes she may not have even been aware of any influence she may have had on the firing decision,"
Ray had submitted his final report to the three-judge panel that oversees his investigation weeks ago. The panel released the report Wednesday after giving parties named in it time to review it and respond.
The White House travel office workers who were fired served at the pleasure of the president and could have been terminated without any reason. But a White House lawyer who worked for then-deputy White House counsel Vince Foster contacted the FBI to pass along rumors of financial improprieties before the workers were fired.
Republicans accused the White House of using the FBI to justify the firings.
The White House conducted an internal review and issued a public apology, saying the firings had been mishandled. It also recommended that five of the seven ex-employees be given new government jobs while it reprimanded four presidential aides. The former head of the office was prosecuted and acquitted of financial wrongdoing.
Ray's predecessor, Kenneth Starr, zeroed in on the travel office in January, 1996, when a memo by Watkins surfaced stating that Mrs. Clinton had been behind the firings.
A year and a half erlier, Mrs. Clinton had denied ordering the dismissals in written answers a White House lawyer submitted on her behalf to the General Accounting Office, the investigative arm of Congress.
"We ... knew that there would be hell to pay if ... we failed to take swift and decisive action in conformity with the first lady's wishes," Watkins wrote in his unaddressed memo, adding that he had been "as protective and vague as possible" in his own answers to investigators.
"Once this made it onto the first lady's agenda, Vince Foster became involved, and he" and Hollywood producer Harry "Thomason regularly informed me of her ... insistence that the situation be resolved immediately by replacing the travel office staff," Watkins wrote. Thomason is a close friend of President and Mrs. Clinton.
The White House internal inquiry concluded Thomason's business partner and friends in the air charter business stood to benefit by reorganizing the travel office, which makes travel arrangements for news reporters and technicians who cover the president.
Ray has said his investigation found that Mrs. Clinton held discussions with Watkins, Foster, Thomason and then-White House Chief of Staff Mack McLarty.
Ray concluded those contacts, which had been known since the original White House review of the firings in 1993, "ultimately influenced Watkins' decision to fire the travel office employees."
The first lady, however, continued to insist she didn't direct the firings. "I had no decision-making role with regard to the removal," Mrs. Clinton said in written answers to Congress in 1996.