The Department of Justice and the FBI have identified over one million compromised computer IP addresses of victims of botnets.
Operation Bot Roast is an ongoing national cyber-crime initiative to disrupt and dismantle 'bot herders' and elevate the public's awareness of botnets.
A botnet is a collection of compromised computers under the remote command and control of a criminal.
"The majority of victims are not even aware that their computer has been compromised or their personal information exploited," said James Finch, assistant director for the FBI's Cyber Division.
"An attacker gains control by infecting the computer with a virus or other malicious code and the computer continues to operate normally.
"Citizens can protect themselves from botnets and the associated schemes by practising strong computer security habits to reduce the risk that your computer will be compromised."
The FBI is working with industry partners including Microsoft and the CERT Coordination Centre at Carnegie Mellon University to notify the owners of the computers.
Through this process the FBI may uncover additional incidents in which botnets have been used to facilitate other criminal activity.
The announcement has been welcomed by security agencies across the globe.
"The FBI's actions in raising the public's level of security awareness regarding botnets and moving against this type of activity are to be applauded, " said Yuval Ben-Itzhak, chief technology officer at web security firm Finjan.
"Our quarterly web security trends reports, for example, have identified botnets as a potentially serious problem for some time now."
The FBI is offering cyber-security tips including updating antivirus software, installing a firewall, using strong passwords, and good email and web security practices.
Although this will not necessarily identify or remove a botnet currently on the system, it can help to prevent future botnet attacks.
The FBI warned that it will not contact infected PC owners online and request any personal information and to be wary of fraud schemes that request this type of information, especially via unsolicited emails.
