Novell on Monday distanced itself from comments last week by Microsoft CEO Steve Ballmer that the Linux operating system infringes on Microsoft patents, although the two companies said that their recently-unveiled alliance remains intact.

"We disagree with the recent statements made by Microsoft on the topic of Linux and patents," Novell CEO Ron Hovsepian wrote in an open letter posted on Novell's site. "Importantly, our agreement with Microsoft is in no way an acknowledgement that Linux infringes upon any Microsoft intellectual property. To claim otherwise is to further sow fear, uncertainty and doubt, and does not offer a fair basis for competition."

A once-bitter rival of Microsoft and creator of the SUSE Linux distribution that competes with Windows, Novell signed an agreement with Microsoft on Nov. 2 in which both companies pledged to make their software work together better, help each other with sales and marketing and protect their corporate customers against possible patent lawsuits.

Microsoft also released a statement on Monday, saying that it "respects Novell's point of view on the patent issue, even while we respectfully take a different view. Novell is absolutely right in stating that it did not admit or acknowledge any patent problems as part of entering into the patent collaboration agreement. At Microsoft, we undertook our own analysis of our patent portfolio and concluded that it was necessary and important to create a patent covenant for customers of these products."

When the Nov. 2 pact was announced, Microsoft executives declined to say whether they felt the Linux OS includes Microsoft intellectual property or otherwise infringes on its patents.

But in a question-and-answer session at a database conference in Seattle on Thursday, Ballmer openly asserted that "Linux uses our intellectual property" and users of the open-source operating system face "an undisclosed balance-sheet liability" as a result.

The comments appeared to confirm the suspicions of open-source community members, many of whom criticized the Novell-Microsoft tie-up, arguing that the deal violates the General Public License (GPL) version 2 under which Linux is licensed, and gives Microsoft ammunition in case it chooses to press its patent claims.

In his letter, Hovsepian reiterated Novell's prior stance that the patent deal with Microsoft does not imply that the Linux source code infringed on Microsoft's patents. "When we entered the patent cooperation agreement with Microsoft, Novell did not agree or admit that Linux or any other Novell offering violates Microsoft's patents. We strongly object to the usage of our agreement to suggest that members of the Linux community owe Microsoft any remuneration."

In a conference call late in the day, Novell and Microsoft executives emphasized that the two companies remain committed to their unlikely alliance. "We are not distancing ourselves from the agreement. We think it's an outstanding agreement," said John Dragoon, chief marketing officer at Novell. "We are not distancing ourselves from Steve [Ballmer]. He can comment however he likes."

"Steve's comments are a perspective we do have at Microsoft," said Dave Kaefer, Microsoft's general manager for intellectual property licensing. He said latent patent violations -- and agreements to indemnify each other against them -- are common.

"Where we compete with some company with similar technology, it is common for there to be overlap," Kaefer said. "It's not because one is a good party and the other is a bad party, it's because we have both created a lot of value."

Kaefer confirmed that the two companies shared their respective patent portfolios with each other before signing the deal, though he said that was also a typical business practice. "We said 'This is what we got.' Both companies were aware of what each other has," Kaefer said.

Neither he nor Dragoon would say how extensive the patent review was, nor whether it turned up any possible violations of Microsoft patents in the Linux source code.

Asked whether Microsoft would consider revealing what parts of Linux allegedly violated the company's intellectual property so that open-source developers could throw out the offending code, Kaefer demurred, saying it would not be "very productive."

"Patents are hard to understand. You have to have a certain level of expertise to understand the scope. And there are legitimate questions about patent quality," he said. "The reality is that you'd have to look at thousands of patents and thousands of products. To focus on every single one would be prohibitive."

Asked whether Linux hobbyists and desktop users should worry about Microsoft suing them, Kaefer said Microsoft "does not have a history of patent litigation," having sued only one company, peripherals manufacturer Belkin Corp., in the last decade.

Dragoon declined to comment on reports that the in-the-works version of the GPL, version 3, will render the Novell-Microsoft deal invalid, calling it "speculation."