Whitaker, 45, who has frequently played golf and basketball with the president while on vacation in Hawaii and other places, was recommended by Obama for the post of director of the Illinois Department of Public Health in 2003 when Obama was an Illinois state senator.
He ran the state health agency until October 2007, when he left to work with Obama's wife Michelle as an executive at the University of Chicago Medical Center. The Sun-Times said grand juries in Chicago and Springfield are investigating "faith-based" initiatives and state-funded health-awareness campaigns Whitaker's agency funded during the administration of former Gov. Rod Blagojevich.
The newspaper obtained copies of the subpoenas under the Illinois Freedom of Information Act.
Whitaker defended his tenure as the state's chief health official in a statement Friday.
"The faith-based outreach programs at issue in this inquiry were recognized during my tenure by the U.S. Centers for Disease Control and Prevention and others as national models for increasing awareness and preparedness planning for minority populations," he said. "The programs were functioning well when I left the department in 2007."
The U.S. attorney's offices in Chicago and Springfield and the White House declined comment, the Sun-Times said.