The highest ranking immigration official in the troubled El Paso region of the southwest border, where hundreds of children were reportedly held for weeks without enough food or the ability to bathe, has been temporarily removed from his job amid growing criticism over health and safety conditions for migrants there.

Aaron Hull, a veteran border official who became the sector chief in El Paso in 2017, will be moved to Detroit on Monday, where he will oversee operations along the much slower and less contentious Canadian border, according to a statement from the agency.

Officials with the Border Patrol’s parent agency, Customs and Border Protection, said Mr. Hull’s transfer was part of a routine shuffle of multiple senior staff members and that Mr. Hull’s new assignment was considered temporary.

But several officials at both the Border Patrol and the Department of Homeland Security said that Mr. Hull’s departure had been long in the works and followed a period of intense scrutiny of his management of the El Paso sector. Mr. Hull did not respond to requests to be interviewed.

The job of overseeing the El Paso region could be considered one of the most difficult within the Border Patrol. Of the agency’s nine enforcement areas along the southwest border, the El Paso region — which stretches from New Mexico into West Texas — has seen the largest increase in unauthorized crossings since last year. So-called family unit apprehensions of migrants who are caught with a relative rose by 1,759 percent in the last fiscal year.

Under Mr. Hull, the El Paso sector was the first to begin conducting widespread family separations with the goal of deterring migrant families from traveling to the United States. Customs and Border Protection piloted the initiative in El Paso during the summer of 2017, roughly a year before the Trump administration publicly announced a nationwide “zero tolerance” border prosecution policy that resulted in widespread family separations.

Agents in the El Paso region told The New York Times that they had been sounding the alarm for some time about conditions in the Border Patrol station in Clint, Tex., where hundreds of migrant children were being held, as well as about other facilities in the El Paso sector where conditions were deteriorating. The agents said their concerns were largely ignored. A spokeswoman from Customs and Border Protection declined to comment on whether the recent controversy in El Paso contributed to Mr. Hull’s transfer.

Mr. Hull is known among colleagues as tough and law-enforcement oriented, according to two D.H.S. officials who spoke on the condition of anonymity because they were not authorized to speak to the news media. One official said that Mr. Hull was seen as part of an “old guard” of border agents, referring to those who have chafed the most as the agency’s job has transitioned away from traditional law enforcement work toward detaining and caring for thousands of migrant children and families.

He resisted attempts from Washington to “meddle” in his sector, one of the officials said. He has often been heard saying that migrants exaggerate the problems they faced in their home countries.

Some agents said the facility in Clint was so filthy that a stench would seep into their clothing and follow them home after they left work, causing friends and family to scrunch their noses when the agents approached. According to lawyers who visited the station and interviewed children who were being held there, some children as young as 7 were caring for infants they had only just met. The children were being overseen by armed guards, the lawyers said, but many of the children were sick, and adult caretakers who could provide treatment were nowhere to be found.

NBC News, which first reported the news about the sector chief’s transfer, obtained a draft report prepared in May by the D.H.S. Office of Inspector General detailing “dangerous overcrowding” at two other facilities overseen by Mr. Hull in the El Paso sector — the El Paso Border Patrol Station 1 and the Paso Del Norte Border Patrol Station.

Investigators found hundreds of adult migrants in the facilities crammed into small cells that were meant to hold only a few dozen. Some of the migrants had gone without sleep because they were left in places where there was standing room only.

Sanitation was also a problem. “With limited access to showers and clean clothing, detainees were wearing soiled clothing for days or weeks,” the report said. There was a “high incidence of illness among staff,” and guards were armed and wore masks because of “concerns with the overcrowding that potentially could result in volatile situations,” such as riots.

The situation was “not sustainable,” the report warned.

In a media tour of the Clint Border Patrol facility in June, Mr. Hull said his agents were doing the best they could with the overwhelming numbers of migrants arriving over the spring, despite being understaffed and underfunded. He said the new arrivals were being processed out of border facilities as quickly as possible.

“When we catch more aliens than we can turn over, they tend to build up here in the station,” he said.

Though the agency did not refer to it as such, Mr. Hull’s move to Detroit was widely viewed as a demotion. It takes him from the El Paso sector, one of the agency’s highest-profile assignments — in part because it is the birthplace of the Border Patrol — to the northern border with Canada, where the pace of activity is much slower.

Mr. Hull will go from overseeing the work of more than 2,000 agents in El Paso to about 400 in Detroit. Though it is the busiest region of the northern border, only about 2,000 people were apprehended in Detroit during the last fiscal year, compared to 31,000 in El Paso.

Taking his place in El Paso will be Gloria Chavez, who presently heads the Border Patrol’s El Centro Sector in southeast California.

Manny Fernandez and Simon Romero contributed reporting.

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