He said he was never bound by his staff's recommendations and that he made decisions based "on the overall" need in the country.
Flores was appointed to the position by President Bush six years ago and has overseen about $1.5 billion dollars in grants during that time.
His former employee, Scott Peterson, said Flores holds daily prayer sessions in the Justice Department office and frowns on giving grant money to organizations that provide sex education or condoms to teenagers.
Instead, said Peterson, Flores favors programs that promote sexual abstinence.
A Washington, D.C. program, Best Friends, that promotes abstinences was awarded $1.1 million by Flores even though it ranked 53rd on a list of 104 applicants.
Best Friends is run by Elayne Bennett, the wife of Bill Bennett, a former Republican cabinet member and now political commentator.
"We're really about positive friendships," she told ABC News at a recent charity gala that included many of Washington's GOP elite. "A good, solid friendship is a beautiful thing," she said.
Murray Waas is a Washington-based investigative reporter who primarily covers national security and law enforcement issues. He is a contributing editor to the National Journal and has also written for the New Yorker, the Los Angeles Times, the Boston Globe and other newspapers and magazines.