Sanchez left Southwest Key earlier this year amid anger over his income and scrutiny of its facilities and processes. Three of the other officials who earned at least $1 million in 2017 also have left the group, according to an official at Southwest Key who spoke on the condition of anonymity because the official was not authorized to comment.

Southwest Key is a prominent contractor housing unaccompanied migrant children awaiting placement with relatives or other adults. It shelters about 4,500 children and teens in Texas, California and Arizona, caring for a little more than a third of the 12,500 minors held by the Department of Health and Human Services.

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This work has proved to be very lucrative: The nonprofit organization has an annual contract of about $460 million to house children, and it has collected more than $1 billion since 2014, according to federal records. Other companies and nonprofit groups also have gotten contracts that could be worth hundreds of millions of dollars apiece for housing children, though some executives have expressed a grim view of their work.

Kevin Dinnin, head of the San Antonio-based nonprofit BCFS Health and Human Services, told reporters at a new emergency shelter for unaccompanied migrant children: “I hate this mission. The only reason we do it is to keep the kids out of the Border Patrol jail cells.”

Sanchez’s compensation ballooned in recent years, nearly doubling from $786,222 in 2015 to $1.48 million a year later. Then it doubled again in 2017, according to the tax form released Tuesday and another filed by a Southwest Key subsidiary that manages charter schools in Texas.

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In a 2018 interview, Sanchez said the increase between 2015 and 2016 came from a retirement contribution rather than a salary bump. He said that in Southwest Key’s early years, they “had nothing. No benefits, no 401(k), no insurance. We just go out there keeping kids out of prisons and jails.”

A representative for Sanchez reached Tuesday declined to comment on his compensation and the tax filing and referred all questions to Southwest Key.

Joella Brooks, who as chief operating officer made more than $1.2 million in 2017 and is now interim chief executive, has said the change in Sanchez’s compensation was because of a life insurance and retirement policy that has since been abandoned.

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After the tax filing was made public Tuesday, Brooks said in a statement that she “and other leaders who participated in the program separately agreed to return substantial portions of the life insurance benefits.”

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In addition to Sanchez, other top officials who made more than $1 million in 2017 and have since left included Jennifer Sanchez, his wife, who had been a vice president, along with another vice president and the chief financial officer.

Brooks said Southwest Key was “moving in a new direction” with a new chief financial officer and that she has asked top officials to reevaluate how they approach compensation.

“These retirement and life insurance programs were designed and implemented by executives no longer with us,” Brooks said. “Those who participated in this program and have left are required to return a significant amount of the retirement portion of the funds that are not vested. We’ve recovered hundreds of thousands of dollars so far.”

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In its tax filings, Southwest Key describes itself as “an integral partner in the U.S. response at our southern border, sheltering immigrant children under 18 years of age who arrive in this country without a parent or guardian and reunifying them with their parents, relatives or a sponsor.”

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The nonprofit organization also said that most of the children in their shelters last year came from Guatemala, Honduras and El Salvador and most were teenage males “fleeing violence and gang threats in their home countries.” Under a section asking for a brief description of its mission, Southwest Key stated: “The mission is opening doors to opportunity, so individuals can achieve their dreams.”