Cybercriminals can control huge networks of computers, called botnets, which can be used to distribute spam, malware and assist with organised crime.
The software giant said Wednesday that it successfully disrupted more than 1,000 networks of computers infected with "malware."
"This cooperative action is part of a growing proactive effort by both the public and private sector to fight cybercrime," Microsoft said in a statement.
The company said the malware affected roughly 5 million people around the globe.
Most computer infections appeared in the United States, Europe, Hong Kong, Singapore, India and Australia.
The FBI said this take-down exemplifies how the public and private sectors can work together, both domestically and internationally, to protect the public from global criminals.
The FBI issued a report this week on the rising use of botnets, which are groups of infected computers controlled by cybercriminals. Criminals can infect a huge network of computers -- numbering in the hundreds of thousands or even millions -- and then each computer is connected to a command-and-control server operated by the criminal.
Botnets can be used to distribute spam, malware and assist with organized crime and terrorist activities, said the FBI.
This is not the first time that Microsoft (Fortune 500) has taken an active role in fighting cybercrime. In March 2012, Microsoft employees, escorted by U.S. Marshals, , raided two U.S. companies and seized servers and hundreds of websites used to steal more than $100 million over five years.
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