But Mr. Sanchez has not entirely left the shelter business behind. He, a friend and Melody Chung, Southwest Key’s former chief financial officer, still own a shelter in Conroe, Tex., through a shell company; the shelter is rented to Southwest Key. Asked by The Times last year about that potential case of self-dealing, in which the executives collected rent paid by the federal government, a Southwest Key spokesman said the partners would seek to sell their ownership stakes. The property has not yet been sold.

Some federal lawmakers have called on the government to cut ties to Southwest Key. Last year, in response to The Times’s reporting, the Department of Health and Human Services said it had commissioned a review of the finances of shelter operators. Asked Monday about the review’s status, a spokeswoman for the agency said she was looking into it.

The enormous compensation for Southwest Key executives came at a time when workers were complaining about a litany of shortcomings in the care of children at the group’s shelters: low-quality food, a lack of books and other teaching materials, insufficient clothing and substandard medical care, according to dozens of interviews with current and former Southwest Key employees in recent months.

Licensed counselors described being given janitorial duties — even being told to paint the walls in new shelters — in addition to their often overcapacity caseloads.

Ms. Brooks said that Southwest Key hired outside experts to talk to hundreds of youths in the group’s shelters, and that the youths reported that they felt safe. She said that to retain their licenses, shelters are required to provide adequate food, clothing and medical care. “Old allegations from former employees don’t match what we and many others see happening in our shelters every day,” she said.

While much of the senior leadership at Southwest Key has resigned this year, the organization’s board of directors, which approved Mr. Sanchez’s compensation, has remained largely intact. One member, Elizabeth S. Villegas, left the board last summer at the peak of the outcry over family separations. On Monday, she said it “wasn’t a good fit for me anymore,” but declined to go into further detail about her reasons for leaving.

Mr. Sanchez, now 71, was a small-town boy made big. He grew up poor in Brownsville, Tex., before becoming the first in his family to go to college, eventually graduating with a doctorate in education from Harvard University. He started Southwest Key in Texas about 32 years ago to help juvenile delinquents stay out of jail.