The Microsoft chief executive told a Q&A session at the Professional Association for SQL Server conference in Seattle that Linux infringed on Microsoft's intellectual property, and that he would not rule out legal action against commercial distributors.
"We have a problem that we have had to confront because of the way the General Public Licence [GPL] works, and because open source Linux does not come from a company," said Ballmer.
"Linux comes from the community, and the fact that this product uses Microsoft's patented intellectual property is a problem for our shareholders.
"We spend $7bn a year on R&D, and our shareholders expect us to protect or licence or get economic benefit from our patented innovations.
"So how do we get the appropriate economic return for our patented innovation, and how do we do interoperability? Because of the complex licensing around the GPL, we did not want to do one without the other."
Leading Linux distributor Red Hat has already dismissed the idea of doing a similar deal with Microsoft, calling such payments an "innovation tax". Red Hat has already indemnified its customers against legal action.
"Red Hat has and will continue to work with Microsoft on true interoperability and open standards in the way we did in advising them in the development of their Open Specification Promise," said the Linux company in a statement.
"At the same time, we do not believe there is a need for or basis for the type of relationship defined in the Microsoft-Novell announcement."
Other open source companies have also condemned Novell for making a deal with Microsoft. In a posting on the Samba.org blog the deal was disparaged as "divisive".
"For Novell to make this deal shows a profound disregard for the relationship that they have with the Free Software community," said the posting.
"We are, in essence, their suppliers, and Novell should know that they have no right to make self-serving deals on behalf of others which run contrary to the goals and ideals of the Free Software community.
"Using patents as competitive tools in the free software world is not acceptable."
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