'Surreptitiously'
The disagreement is based on Symantec's Volume Manager software, which allows operating systems to store and handle large amounts of data.
Symantec believes Microsoft has "deliberately and surreptitiously misappropriated" the technology "and thereby convinced the US government to issue patents to Microsoft based on technologies invented by Symantec".
For its part, Microsoft says it licensed the technology from Veritas Software, a company that Symantec acquired last year in a $13.5bn (£7bn) deal.
"We are confident that our actions are wholly consistent with the legal agreements between Veritas and Microsoft and that these claims will be shown to be without merit," Microsoft said in a written statement.
Symantec produces Norton software, a package used to protect computers from being hacked into.
The news comes as Microsoft intends to launch its own internet security software.