Speaking in Microsoft's Asian Government Leaders Forum in Singapore, Ballmer reiterated the controversial claim that Linux violates more than 228 patents, according to Reuters.
"Someday, for all countries that are entering the WTO (World Trade Organisation), somebody will come and look for money owing to the rights for that intellectual property," Ballmer reportedly said.
This statement didn't impress Novell which -- like Microsoft -- owns a very large number of software patents.
"The intellectual property risks associated with open-source software are really no greater than those with proprietary software and so far, nobody has filed any patent claims against open source," said Bruce Lowry, Novell spokesperson.
"Novell provides indemnity protection against legal action for our customers and we are committed to using our own patent portfolio to protect our open source software offerings," Lowry added.
Last month Novell chief executive Jack Messman declared that his company would use its patent portfolio to defend customers who used its open source software.
Gael Duval, founder of Linux vendor Mandrakesoft, accused Ballmer of scare tactics, and argued that Windows users were just as much at risk as Linux users.
"Again [we have] some fear, uncertainty and doubt from Microsoft. They do whatever they can to fight against Linux," Duval said.
"On the other hand, Microsoft is involved in a number of patent trials, so governments who use Microsoft products face patent lawsuits no more and no less than for Linux products," Duval added.
Stuart Cohen, chief executive of the Open Source Development Labs (OSDL), said his organisation had a lot of confidence in Linux's robustness when it came to IP, patents and copyright.
"Some of the world's largest vendors share our view and are willing to stand behind Linux to protect their customers, as are we. HP offers its Linux customers indemnification. So do Red Hat and Novell. Both Novell and IBM have publicly promised to use their extensive patent portfolios to protect Linux customers," said Cohen.
"And OSDL set up a $10m legal defence fund for Linux customers. With Linux adoption growing three times faster on the server than any other operating system, customers are clearly continuing to embrace Linux," Cohen added.
Microsoft was not immediately able to expand on Ballmer's remarks, which have sparked speculation that they represent Microsoft's plans for litigation against Linux.
Ballmer stopped short of saying that Microsoft itself would be suing Linux users, and also did not say who owned the patents in question. Previous reports have claimed that Linux violates 283 patents.
Analysts believe Ballmer's remarks could actually rebound on Microsoft.
"The impression that customers will get from these sort of comments will do nothing to move them closer to a mature and strategic relationship with Microsoft," said Rakesh Kumar, senior vice-president at META Group.
"Users are intelligent enough to assess their own risks. Microsoft needs to build bridges with international organisations rather than being abrasive," Kumar added.
If Ballmer's remarks do represent a turning point in its battle with Linux, then it is heading for explosive confrontations with several other IT giants.
On Wednesday, Sun chief executive Scott McNealy said his company was ready for war over the issue of intellectual property litigation.
McNealy told ZDNet UK sister site ZDNet Australia the recent Kodak patent case was an example of the company "taking a bullet" to protect its end-users.
"Customers need to use a software provider with cash in the bank, who protects and indemnifies them and will look out for their interests," McNealy said.
When asked how many bullets Sun could take, McNealy said the company had $7.4bn in the bank, strong growth and an "IP war chest" that "scares a lot of companies away". McNealy did not rule out a patent war, but was confident of Sun's position should one occur.
Brendon Chase of Builder AU contributed to this report