Also listed in the criminal complaint was Karen Anne Christiansen, a director of planning and facilities with Beverly Hills Unified at the time. Christiansen, 52, now living in Las Vegas, is expected to be extradited to California, Schmidt said.
Hubbard vehemently denied the allegations.
"It's absolutely not true," Hubbard said, becoming emotional during an interview at the door to his apartment near Fashion Island on Thursday night. "It's an injustice. This is my career. It's just not right. I don't know how I could have anything to do with it."
Bail for Hubbard, 53, who started as Newport-Mesa Unified's superintendent in July 2006, was set at $50,000.
Christiansen's bail has been set at $2 million. She faces two counts of misappropriation of funds and six conflict-of-interest counts, Schmidt said.
According to the complaint, Christiansen received an unauthorized stipend of $20,000 from Hubbard — something that later was allegedly discovered by the Beverly Hills district's assistant of business services superintendent, Alex Cherniss.
In addition to the stipend, Hubbard allegedly gave Christiansen increases in her car allowance that were unauthorized by the Beverly Hills school board, according to the criminal complaint.
Christiansen was hired as a facilities director for the Beverly Hills district in 2004 at an annual salary of $113,000. But in 2006, she allegedly negotiated a secret contract to be an independent contractor while also performing her school district duties — a violation of state conflict-of-interest codes, Schmidt said.
As a result, she was paid $5.2 million by the school district from 2006-09, a contract that Hubbard said was approved by the school board after he left.