Kelley says the FBI and the Department of Defense violated her privacy. She accuses them of wrongfully searching her personal emails and providing the media with false and defamatory information.
Kelley's name first came to light after the CIA director admitted to an affair with his biographer, Paula Broadwell, and resigned his position.
Kelley had complained to law enforcement officials about threatening emails from Broadwell. Kelley and her husband, Scott Kelley, are pushing for an apology and unspecified damages in the lawsuit filed Monday.
The lawsuit claims the federal government violated the Privacy Act. It also claims that government officials violated the Constitution's ban on unreasonable searches in its review of Kelley's emails. The Kelleys claim they have suffered financial losses because of the government's actions.
The Associated Press contributed to this report.