According to the consumer protection groups, FastMP3Search.com, is a fake music search site that asks consumers to install a plug-in to be able to download MP3 music files, but actually cons them into downloading malicious applications leaving their PCs vulnerable to further hacking attacks.
The complaint will state that the free download disables the Windows firewall, alters homepage settings, changes website addresses for legitimate security companies and affects the PCs performance.
Furthermore, StopBadware.org claims the downloads are made without the user's consent and are difficult to uninstall.
John Palfrey, co-director of StopBadware.org, said in a statement: "In the past year, we have come across dozens of malicious programs available on hundreds of websites, and without question, FastMP3Search.com tops our list of the worst actors."
He added: "They have combined so many things in a single bundle. It's a parade of horribles."
The complaint will seek immediate action from the FTC against the website and it's owners and operators.
Last month the FTC fined the online advertising company, Zango, £2 million for "unfairly and deceptively" installing adware more than 70 million times onto people's computers.
StopBadware.org is an initiative that aims to produce a blacklist of malicious sites and the CDT is a watchdog group that runs the Anti-Spyware Coalition.