“The logical thing to do to maximize safety and minimize waste of public funds would not be to immediately shut down an enormous number of shelters,” Ms. Cancian said. “The best course of action would be to figure out a plan for transitioning those facilities and transitioning those personnel.”

The Office of Refugee Resettlement, the agency that oversees migrant shelters as part of the Administration for Children and Families, declined to speculate on Southwest Key’s grants. In response to a question asking if the agency had a plan if the charity were to lose its grants, a spokeswoman said the agency was always planning for unforeseen events.

A Southwest Key spokesman, Jeff Eller, said the charity had had no discussions about losing its grants with the Office of Refugee Resettlement or about its shelter licenses with officials from Texas, Arizona or California. He said the charity was focused on providing “the best care possible” for children.

Last year, the government cut off the contracts of another major shelter provider, International Educational Services, over suspected financial improprieties. Juan Sanchez, who founded Southwest Key and still runs it, also helped establish I.E.S., although he has not had a role there for decades.

The closing of I.E.S. facilities was carried out haphazardly, straining the system for months. As many as 620 children needed to be rehoused; most landed in Southwest Key facilities.

Comprehensive Health Services, a for-profit company based in Florida that ran one of the temporary shelters, leased three former I.E.S. shelters, all in the Rio Grande Valley in Texas, and then received a new government contract. Many original staff members were rehired.