The complaint concerns the privacy implications of the forthcoming Microsoft XP operating system and how it integrates with Passport, Microsoft's online authentication service.
The Electronic Privacy Information Centre believes XP will leave users with little option other than to employ Passport. The centre maintains that Passport has the ability to obtain personal information about users without their consent.
Marc Rotenberg, the executive director of EPIC, said: "We're planning to file the complaint today. The FTC has jurisdiction over Microsoft if it is found to fail to comply with Safe Harbour."
Microsoft is a co-signatory to the Safe Harbour agreement, which specifies the ways in which US companies must satisfy the European Directive's requirements concerning data protection principles.
The directive states that the transfer of information concerning European citizens will be prohibited to non-EC countries that adopt inadequate privacy practices.
Epic has already joined 12 other consumer and privacy groups in filing a complaint to the FTC asking it to investigate Passport and XP. James Mullock, a partner in Osborne Clarke's IT and telecoms group, said: "This is a hot potato for Microsoft. There are a number of obligations Microsoft will have to meet in Europe under Data Protection legislation.
"Safe Harbour is only one of them. Where you are acquiring information, as with Passport, you must tell the user who will ultimately be using the information and how they will use it, as well as getting their consent."
Phil Jones, assistant information commissioner at the government office responsible for data protection, said: "We are not aware of any complaints, but we will keep an eye on developments. Companies are usually fairly sensitive to criticism of this kind and take steps to address it. The problem is that XP has not been released yet so nothing has gone wrong yet."
A Microsoft spokeswoman refused to comment on the case.