It came in a 249-page brief submitted to a US appeals court as the firm began its battle to overturn a court ruling that it broke competition laws and must be split in two.
It said there had been "numerous factual, legal and procedural errors in the case".
In response, US justice department spokeswoman Gina Talamona said the judgement was "well supported by the evidence offered during a 78-day trial, including thousands of pages of Microsoft's own documents".
Attacking the judge
Microsoft also said that the split ruling by US district Judge Thomas Penfield Jackson "would stifle innovation and harm, not help, competition."
The firm attacked Judge Jackson for his comments outside the courtroom.
"By repeatedly commenting on the merits of the case in the press, the district judge has cast himself in the public's eye as a participant in the controversy, thereby compromising the appearance of impartiality, if not demonstrating actual bias against Microsoft," the firm said.
This behaviour was "emblematic of the manner in which he conducted the entire case - employing improper procedures and changing the rules of the game, always to Microsoft's detriment" said the submission.
Microsoft maintains that its conduct in competing with Netscape "was unambiguously pro-competitive: it benefited consumers by lowering prices, ensuring widespread availability of new technology, and accelerating product improvement".
Browser battles
Netscape Navigator was the standard browser used by computer users to surf the internet until Microsoft's Internet Explorer took over.
Judge Jackson's ruling was that Microsoft abused its dominant position in the personal computer operating system market to bully its way to leadership in the browser market.
The original court heard examples of threats or rewards offered to computer manufacturers and rival software firms by Microsoft to ensure its products and internet browser were favoured over Netscape.
The government is due to file its brief to the court on 12 January, with Microsoft having a chance to reply by the end of that month.
Court hearings in the latest stage of the case are scheduled for the end of February.
Judge Jackson and the US Justice Department had wanted the case passed directly to the Supreme Court, but the high court turned that plea aside.