Neelie Kroes, competition commissioner, said: "Microsoft was the first company in 50 years of EU competition policy that the Commission has had to fine for failure to comply with an antitrust decision."
Microsoft has said it has been making every effort to comply with the commission's orders.
However, Kroes said: "Talk is cheap, flouting the rules is expensive. We don't want talk and promises. We want compliance."
'Dark chapter'
Microsoft said the fines concerned "past issues" and it was now looking to the future.
In its 2004 ruling, the commission said Microsoft's rivals saw their markets shrivel because Microsoft stopped providing the information they needed to link up to Windows office machines.
Microsoft had then stepped in and replaced its rivals' offerings with its own products.
Microsoft was ordered to provide the information, but imposed high royalties on grounds of innovation.
The commission said the information did not show such innovation and that the large royalties were unjustified.
Kroes said: "I hope that today's decision closes a dark chapter in Microsoft's record of non-compliance with the commission's March 2004 decision."
New investigations
Last week, Microsoft promised to publish critical information so that rival programmes worked better with Windows.
That came as the company was facing this week's fine and following two new formal commission investigations which opened in January.
The new commission investigations relate to the issues of the 2004 case but with different products.
Kroes took a wait-and-see attitude about Microsoft's announcement of last week, noting it had promised change on four other occasions without results.
She said: "A press release, such as that issued by Microsoft last week on interoperability principles, does not necessarily equal a change in a business practice."