Prison director Orlando Saucedo Pinto was put on temporary leave pending an investigation into how the prisoners got away, Mexican prison officials said at a news conference. Prison staff were also being investigated, they said.
The federal Attorney General's Office said in a statement Thursday night that 40 prisoners escaped, while local authorities had earlier put the number at 41.
Fifty prison employees were being held for questioning, the statement added.
The office said all the prisoners who escaped had been charged under federal law but were being held at the state institution. Five were serving sentences following convictions and 35 were on trial. The statement did not specify the offenses, but drug trafficking is among the most common federal charges.
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State leaders in Mexico have complained in the past that they do not have facilities secure enough to accommodate more serious, federally charged prisoners.
Last year guards stood by as more than 50 prisoners walked out of another jail in northern Mexico.
Eddie Perez, a spokesman for the U.S. Customs and Border Protection in Brownsville, said agents at the border were on alert because of the prison escape.
"We do have a contingency plan in effect, and we will do anything that we can to ensure the safety of the traveling public and our officers," he said.