Mexican President Andres Manuel Lopez Obrador said authorities believed the blaze in the city opposite El Paso, Texas, broke out at 9.30pm On Tuesday as some migrants set fire to mattresses in protest after discovering they would be deported. He did not provide more details about how so many had died in the incident.
"They didn't think that would cause this terrible tragedy," Lopez Obrador told a news conference, noting that most migrants at the facility were from Central America and Venezuela.
The fire, one of the deadliest to hit the country in years, occurred as the United States and Mexico battle with record levels of border crossings at their shared frontier.
Twenty-eight of the dead were Guatemalans, Guatemala's national migration institute said, while 13 were Hondurans, according to the country's deputy foreign minister. It was not immediately clear why those totals differed from the death toll given by Mexican authorities.
A Reuters witness at the scene overnight saw bodies laid out on the ground in body bags behind a yellow security cordon, surrounded by emergency vehicles. The fire had been extinguished.
In addition to the 40 who died, 28 others were hospitalised after being injured in the blaze, Mexico's National Migration Institute (INM) said. All were adult men, officials said.
It's not immediately clear how the fire was managed, if there were emergency exits or what protocols officials took to deal with protests.
Activists have frequently flagged concerns of poor conditions and overcrowding in detention centres as migration has risen.
"Last night's events are a horrible example of why organisations have been working to limit or eliminate detention in Mexico," said Gretchen Kuhner, director of the Mexico-based Institute for Women in Migration, which supports migrant rights.
Mexico's INM did not respond to a request for comment about when the Ciudad Juarez site was opened, or how many migration centres are currently in operation.
As of 2019, there were 53 INM detention centres operating across Mexico, according to a report from Mexico's Human Rights Commission (CNDH), with a total official capacity of around 3000.
The nyumbers of migrants in Mexican border cities have built up in recent weeks as authorities attempt to process asylum requests using a new US government app known as CBP One.
Many migrants feel the process is taking too long and earlier this month clashes occurred between US security and hundreds of mostly Venezuelan migrants at the border after frustration welled up about securing asylum appointments.
Mexico's migration law says migrants can only be detained for 15 days under normal circumstances, though the Supreme Court in March ruled that such lengths were unconstitutional, and that migrants should be held no longer than 36 hours.
In January, the Biden administration said it would expand Trump-era restrictions to rapidly expel Cuban, Nicaraguan and Haitian migrants caught crossing the US-Mexico border in an effort to contain the border flows.
That came after a decision in October to the expand expulsions, under a controversial policy known as Title 42, to Venezuelans.
At the same time, the United States said it would allow up to 30,000 people from those countries to enter the country by air each month.
