Microsoft is investigating a trojan program that attempts to switch off the firm's anti-spyware software.
Microsoft is under pressure to close security holes
The spyware tool was only released by Microsoft in the last few weeks and has been downloaded by six million people.
Stephen Toulouse, a security manager at Microsoft, said the malicious program was called Bankash-A Trojan and was being sent as an e-mail attachment.
Microsoft said it did not believe the program was widespread and recommended users to use an anti-virus program.
The program attempts to disable or delete Microsoft's anti-spyware tool and suppress warning messages given to users.
It may also try to steal online banking passwords or other personal information by tracking users' keystrokes.
STAYING SAFE ONLINE
Install anti-virus software
Keep your anti-virus software up to date
Install a personal firewall
Use Windows updates to patch security holes
Do not open e-mail messages that look suspicious
Do not click on e-mail attachments you were not expecting
Microsoft said in a statement it is investigating what it called a criminal attack on its software.
Earlier this week, Microsoft said it would buy anti-virus software maker Sybari Software to improve its security in its Windows and e-mail software.
Microsoft has said it plans to offer its own paid-for anti-virus software but it has not yet set a date for its release.
The anti-spyware program being targeted is currently only in beta form and aims to help users find and remove spyware - programs which monitor internet use, causes advert pop-ups and slow a PC's performance.