As a result, the software maker would be forced to provide a royalty-free licence for its intellectual property to developers and users of all Linux distributions. The FSF considers Microsoft's refusal a copyright violation.
"We will ensure that Microsoft respects our copyrights and complies with our licences," the FSF said in a statement on Tuesday.
The claim echoes earlier statements by the open source advocacy group claiming that Microsoft is a distributor of Linux code and is therefore subject to the GPLv3.
The case leads back to last year's Microsoft-Novell partnership in which Microsoft purchased 70,000 coupons for Novell's SuSE Linux software and patent licence. The coupons are currently being distributed to Microsoft customers.
Although Novell ships and supports the software, the question hinges on which company distributes the software.
Microsoft claims that it is Novell, but the FSF argues that Novell is merely acting as a fulfilment agent, as proven by the $240m that Microsoft paid Novell for the coupons.
The FSF opposes Microsoft's patent pledge that is limited to SuSE customers. The promise divides the open source community between those who are willing and able to pay for the licence and those who are not.
The arrangement also rewards Microsoft for intellectual property which the FSF considers worthless.
The group responded by adding a provision to the GPLv3 designed to sabotage the exclusive licences.
If a distributor of GPLv3 software provides a patent pledge to one GPLv3 user, that promise is automatically extended to all users and developers of that application.
These include several components that ship as part of the Linux operating system that will eventually end up in commercial Linux distributions including SuSE.
Microsoft did not take long to counter the GPLv3. The software vendor unilaterally changed the conditions for the Novell SuSE certificates in July, excluding the vouchers from providing support for GPLv3 code.
Microsoft also continues to argue that it does not distribute the SuSE software.
Novell, meanwhile, has promised that it will honour the certificates regardless of Microsoft's actions. Legal experts are debating whether Microsoft is able unilaterally to change the terms of the coupons.
A spokesperson for Microsoft declined to comment on the latest FSF statement.
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