State police said Freeh was taken by helicopter to a New Hampshire hospital following the crash Monday in Barnard, a small town about 90 miles northwest of Boston.
Information about Freeh's condition was not made public. His name was not on a list for which patient information was available, according to Dartmouth Hitchcock Medical Center.
Freeh apparently drove his SUV off the road shortly after noon and struck a mailbox and a row of shrubs before coming to a stop on the side of a tree, state police said. He was wearing his seatbelt.
The cause of the crash is still under investigation, police said. No one else was hurt.
"The thoughts and prayers of the entire FBI remain with former Director Freeh and his family tonight," FBI Director James Comey said in a statement.
Freeh, 64, was a federal judge in New York before serving as FBI director from 1993 to 2001. He previously served six years as a special agent. He founded his consulting firm, Freeh Group International Solutions LLC, in 2007.
In 2011, Penn State hired Freeh to examine the handling of child sex abuse complaints involving former assistant football coach Jerry Sandusky and to recommend changes aimed at preventing abuse.
Following an eight-month, $6.5 million investigation, Freeh issued a blistering report contending that legendary head football coach Joe Paterno and other top Penn State officials concealed what they knew about Sandusky's sexual abuse of children for more than a decade ago to avoid bad publicity.
Sandusky was convicted in June 2012 on 45 criminal counts.
Freeh also has handled other high profile matters, including a bribery case involving FIFA's presidential election and a review of the financial settlement program for Gulf Coast residents affected by the BP oil spill.