Canonical has followed in the footsteps of Red Hat, the largest Linux vendor, by rejecting calls to form a pact with Microsoft.
Microsoft already has tie-ups with Red Hat's rival Novell and smaller open-source firms Xandros and Linspire.
Red Hat told ZDNet.co.uk on Monday that it would form no such agreement with Microsoft.
Mark Shuttleworth, Canonical's chief executive, wrote in a blog that Canonical has declined to talk to Microsoft about any agreement that provides legal protection to Ubuntu users related to "unspecified patents".
"Allegations of 'infringement of unspecified patents' carry no weight whatsoever. We don't think they have any legal merit, and they are no incentive for us to work with Microsoft on any of the wonderful things we could do together," he wrote.
Shuttleworth said these patent agreements create "a false sense of security" and do not effectively protect the user from a patent suit from a big company like Microsoft.
In the same blog post, Shuttleworth said pursuing technical interoperability between rival document formats Office Open XML and OpenDocument — included in the other Linux deals — was not worth the effort. He did say, however, that Ubuntu stands to benefit from investments to improve interoperability between Linux and Windows.
"I have no confidence in Microsoft's Open XML specification to deliver a vibrant, competitive and healthy market of multiple implementations. I don't believe that the specifications are good enough, nor that Microsoft will hold itself to the specification when it does not suit the company to do so," Shuttleworth said.
OpenDocument Format (ODF) is better and Microsoft should improve its support for that standard, Shuttleworth said.
Shuttleworth did not rule out working with Microsoft in some capacity but made clear that the make-up of its existing Linux partnerships held little interest for Canonical. "All the deals announced so far strike me as trinkets in exchange for air kisses," he said.
Canonical is a commercial company that sponsors free-software projects and provides services for the Ubuntu Linux distribution.
Martin LaMonica writes for ZDNet.co.uk's sister site CNET News.com