State officials are launching an audit of six Minnesota autism treatment centers to find out if they've been properly billing the government for millions of dollars in children's therapy.

The audit is designed to explain why a handful of treatment programs have been charging Medicaid tens of thousands of dollars more, per child, than their competitors, said Anne Barry, deputy commissioner of the Department of Human Services.

"We have to look deeper because we're not satisfied with the answers we're getting right now," Barry said.

The audit was triggered, in part, by reports in the Star Tribune last year that Medicaid paid an average of $36,000 per child for "skills training" at centers that specialize in an intensive treatment known as ABA (applied behavior analysis). The payments were roughly three times the state average for skills training.

The state insists it does not cover ABA treatment itself -- which can run up to 40 hours a week and cost $100,000 a year per child. But officials could not explain why Medicaid did pay for hundreds of hours of "skills training" for children in ABA programs -- an average of 770 hours in 2010, at a cost of $13.5 million. By comparison, autistic children in Medicaid HMOs received 39 hours of skills training.

Barry said the agency decided to launch the audit after conducting an initial review last year. "We looked for any kind of rationale or justification," Barry said, but couldn't find anything "that would justify the differences."

She said the federal agency that oversees Medicaid -- and pays half the program's cost -- has endorsed the audit. "They're concerned about the same things we are," she said. She said the audit process would be more intense, involving on-sight visits and a review of medical records. If it finds inappropriate payments, the agency could move to recover the money.

Last week, the agency sent audit notices to five programs that specialize in ABA: the Lovaas Center, Behavioral Dimensions, Minnesota Autism Center, the Lazarus Project, and the Rochester Center for Autism. It also sent a notice to the state's largest autism treatment center, Fraser.

Officials at several of the centers said they welcome the audit. "I feel like we're providing a good program, and we're operating under the statutes and doing that in good faith," said Jon Sailer, owner of the Rochester Center for Autism. At the same time, he said, "any time there's a question of stopping or reducing billing, that's obviously a concern."

Eric Larsson, who heads the Lovaas Center in Minneapolis, acknowledges that his program is more costly than others. "We only work with families that want high-intensity treatment," he said. "It's what we're known for." State records show that Medicaid paid Lovaas an average of $70,000 per child for skills training in 2008, more than any other center, and six times the state average. "When people come to audit us ... we always get really high marks," he said.

Diane Cross, president of Fraser, said she's not sure why the state is auditing her program, which offers a broader array of therapies than the ABA centers. But she noted that the DHS "is very strict on what you're allowed to do and not do," and that audits are routine.

Some advocates, though, fear the state may cut off access to some of the most expensive, and intensive, autism treatments. Several autism centers say that more than half their clients get Medicaid funds.

"There are hundreds of kids who are going to be negatively affected right away if there's a change," said Amy Dawson, who runs the Autism Advocacy and Law Center in Minneapolis. She said many families have turned to the state to pay for intensive therapy because most private insurers won't cover it.

If Medicaid shuts the door, she said, "then families for the most part will be left with nowhere to turn." At that point, she said, the battle may switch to the public schools, with parents demanding higher levels of services for autistic students. "And I will suddenly be very busy suing school districts," she said.

Maura Lerner • 612-673-7384