“This seemed to be a really nice retention tool,” Ms. Fava said. “It had a quality to it, we’re going to help you pay for your kids’ college. So, sure, we could have increased their salary or given them a bonus. But this had a nicer, you know, cultural component to it.”

The report also noted that a Young Adult Institute affiliate, the New York League for Early Learning, had paid the Levy brothers consulting fees of about $50,000 a year from 2007 through 2009, on top of their salaries. And it questioned other expenses, including lunches and dinners for executives and the $1,468 that Philip Levy spent to stay for two nights at the Beverly Hills Hotel in 2008, which he said was for a meeting with a possible donor.

The commission, which has no enforcement powers, suggested that the organization’s board “consider carefully” whether certain expenditures “are compatible with the obligation of the board to act as a faithful steward of public funds.” More than 95 percent of the organization’s revenue comes from government sources, primarily Medicaid.

In June, two days after The Times e-mailed a Young Adult Institute spokesman seeking more detail about the tuition program, the Levy brothers ended their employment there. The organization announced the departures two weeks later in a press release, saying Philip Levy was retiring, but quoting him as saying he was looking forward “to a new stage of my career.” The spokesman, Jesse Derris, said that Joel Levy’s departure as a consultant had been expected, and that Philip Levy had been unable to come to terms on a new contract with the group’s board.

The Levys appear to be financially well prepared for the next phase of their lives. Each received deferred compensation totaling about $1.8 million in 2008 and 2009.

Courtney Burke, commissioner of the Office for People With Developmental Disabilities, last week took a step toward reining in high executive salaries at the nonprofit groups. She sent a one-page letter to them on Tuesday seeking their assistance to develop “a consistent and rational model of compensation.”

“Given the heightened concerns about the growth of Medicaid and Medicare, this compensation guidance should be established sooner rather than later,” she wrote.