The world's largest software maker has also identified at least another 4.7 million infected machines, though many are likely still controlled by cyber fraudsters, Microsoft's cybercrime-fighting Digital Crimes Unit said on Thursday.
India, followed by Pakistan, Egypt, Brazil, Algeria and Mexico have the largest number of infected machines, in the first high-profile case involving malware developed outside Eastern Europe.
Richard Domingues Boscovich, assistant general counsel of the unit, said Microsoft would quickly provide government authorities and Internet service providers around the world with the IP addresses of infected machines so they can help users remove the viruses.
"Those victims are currently not aware they are infected," Boscovich said in an interview.
The operation is the most successful of the 10 launched to date by Microsoft's Digital Crimes Unit, based on the number of infected machines identified, Boscovich said.
Microsoft located the compromised PCs by intercepting traffic headed to servers at Reno, Nevada-based Vitalwerks Internet Solutions, which the software maker said criminals used to communicate with compromised PCs through free accounts on its No-IP.com services.
Vitalwerks criticized the way Microsoft handled the operation, saying some 1.8 million of its users lost service for several days. The Internet services firm said that it would have been glad to help Microsoft, without interrupting service to legitimate users.
Microsoft has apologized, blaming "a technical error" for the disruption, saying service to customers has been restored.
The operation, which began on June 30 under a federal court order, targeted malicious software known as Bladabindi and Jenxcus, which Microsoft said work in similar ways and were written and distributed by developers in Kuwait and Algeria.
© Thomson Reuters 2014