The software giant is notifying Web developers and other partners on Friday that it is changing the way Internet Explorer handles certain Web programs, known as ActiveX controls and Java applets.
With the change, Web developers will need to slightly modify their pages or consumers will have to make an extra click to get to some content, such as for a Macromedia Flash-based advertisement.
"We think that the user experience impact is relatively modest," said Michael Wallent, a general manager in Microsoft's Windows-client unit.
Microsoft will incorporate the new version of Internet Explorer into all new copies of Windows and also into the next version of the browser, IE 7, which will be available for Windows XP, Windows Server 2003 and as part of Windows Vista. Existing users may also get the new code as part of future security updates, Wallent said.
"We believe over the next six months, most customers will be running copies of Internet Explorer with this behavior."
Microsoft has been in a long-running spat with Eolas Techologies and the University of California. In September, the U.S. Patent Office
A University of California spokesman said that its lawsuit against Microsoft deals with infringement caused by previously sold versions of the browser.
"The lawsuit covers sales predating this latest reconfiguration," he said.
In 2003, a juryin damages to the university and Eolas, but Microsoft appealed the decision. An appeals court this year Microsoft's stance, saying the company should be allowed to present evidence that similar inventions predated Eolas' patent application.
"We believe this change insulates us from any potential liability," Wallent said. "We don't expect we will have to make any other changes.
Wallent said that the move was designed to end uncertainty for the future as the Eolas case heads back to court later this year.
"With this change we are very confident that we would no longer have liability even if the case doesn't go our way in the end," he said.
Wallent added that Microsoft's move "in no way reflects a lack of confidence in our case."
"We'll continue to pursue our case and believe that the Eolas patent is invalid," he said.