The indictment accuses Stadd of steering money from an earth science appropriation to Mississippi State University, which was paying him as a consultant. Stadd is also accused of lying to NASA ethics officials investigating the matter.
He faces up to 15 years in prison if convicted on all three charges.
NASA officials on Friday declined to comment on the indictment. Stadd, who joined NASA as chief of staff in 2001 and left the agency in 2003, was President George W. Bush's NASA transition chief in 2000. Stadd "was centrally involved in the organization and management of NASA," said John Logsdon, a Smithsonian Institution space scholar.
"He was in many ways the White House representative to the NASA front office," said Logsdon, a member of the NASA Advisory Council. "So he had a fair degree of influence."
When Stadd announced that he was leaving, then-NASA chief Sean O'Keefe said, "Courtney has been a faithful public servant and a creative leader who knows how to motivate people and get things done."
According to the indictment, Stadd started a management consulting firm called Capital Solutions that specialized in advising aerospace-related clients, including Mississippi State University's Georesources Institute.
The institute paid Stadd $85,000 in fees and travel costs to provide technical document editing and prepare community outreach and public communications material, the indictment says.
George Washington University professor Scott Pace, a former NASA associate administrator and Stadd's former deputy, said the indictment was "bizarre." He said it didn't fit with the conscientious and ethical person he knows Stadd to be.
Stadd returned to NASA as a consultant in 2005 to help with the transition from O'Keefe to new NASA administrator Michael Griffin, Pace said.
A NASA spokesman said Stadd was paid $112,100 when he was hired in 2001 and then got a raise to $133,700 before leaving in 2003. His consultant work was at a $107,120 annual salary, but he was only in the position three months, the spokesman said.
In an April 19, 2005 memo, Griffin said he was creating a new job of associate administrator to run the agency's day-to-day operations, and that Stadd was going to temporarily serve in the spot until it was filled. The indictment says Stadd worked in the NASA administrator's office for the next three months.
The indictment says Stadd disclosed to NASA officials upon his return that the university was one of his clients, but said he was recusing himself from any agency activities related to the client. Yet the indictment accuses Stadd of using his position in the administrator's office to steer $12 million of $15 million that Congress appropriated for NASA's earth science program to Mississippi, with Mississippi State ending up with $9.6 million through five subcontracts.
"If I intervene anymore then (sic) all sorts of red flags will go up and I fear getting MSU and me in trouble," Stadd wrote in an e-mail to a university official quoted in the indictment.
Mississippi State said when it received the grant that it was using the money to develop a "Google for NASA research" - a computerized, one-stop database for Earth science research that could impact climate change, bioterrorism, transportation and population trends.
Three months after leaving his temporary position in the NASA administrator's office, Stadd sent an e-mail to a Mississippi State official proposing that his consulting fee be increased from $3,000 a month to $7,000-$10,000, according to the indictment. In an excerpted e-mail, Stadd wrote the NASA contract was an example of "the return on the investment" that the university got for his services. The university gave him another contract worth up to $60,000, the indictment says.
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AP Science Writer Seth Borenstein contributed to this report.
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