The images, apparently taken by the actress, follow the leaking of naked photos of stars including Jessica Alba.
The FBI said it was investigating "the person or groups responsible for a series of computer intrusions involving high-profile figures".
A spokeswoman for Johansson was not available for comment.
Hacked photos of Justin Timberlake and his Friends With Benefits co-star Mila Kunis have also appeared online, according to reports.
Laura Eimiller, of the FBI's Los Angeles office, said dozens of stars had been the victims of hackers who had stolen personal information from email and other accounts.
She did not name any alleged victims "due to the pending nature of our investigation".
One leaked photo appears to show Johansson topless on a bed while another apparently shows her wearing a towel while revealing her bottom.
According to US celebrity website TMZ.com, Johansson has contacted the FBI over the leak.
TMZ also reports that her lawyer has sent letters to websites stating that Johansson owns the copyright to the pictures and threatening legal action if they are not removed.
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