CIA Director John Brennan’s private account held sensitive files — including his 47-page application for top-secret security clearance — until he recently learned that it had been infiltrated, the hacker told The Post.

Other e-mails stored in Brennan’s non-government account contained the Social Security numbers and personal information of more than a dozen top American intelligence officials, as well as a government letter about the use of “harsh interrogation techniques” on terrorism suspects, according to the hacker.

The FBI and other federal agencies are now investigating the hacker, with one source saying criminal charges are possible, law-enforcement sources said.