The charges accuse Siegelman and former Chief of Staff Paul Hamrick of helping a Tuscaloosa businessman rig bids for a maternity care program while Siegelman was governor.
The charges involve allegedly moving $550,000 from the state education budget to the State Fire College in Tuscaloosa, so Tuscaloosa physician Phillip Bobo could get the money and offer it to a competitor not to seek the maternity care contract.
"I was blindsided by these charges," said Siegelman from his Birmingham office. "I was never asked a single question and never given the opportunity to give a single answer. These charges are baseless and I am innocent."
Siegelman, a Democrat, said the indictment is politically motivated, calling it "Republican politics at its worst".
CNN contributed to this report.