Mr Kerik, the city's top police officer at the time of the 9/11 terror attacks, was indicted by a federal grand jury.
He has been charged with 14 offences, including fraud, obstructing an FBI investigation and lying to the federal government, a US attorney said.
The matter is awkward for presidential hopeful Rudy Giuliani, who backed Mr Kerik to run homeland security in 2004.
President George W Bush nominated Mr Kerik for homeland security in part on the strength of Mr Giuliani's recommendation.

