Treasury minister Luis Videgaray has resigned, a ministry spokeswoman said, the week after Donald Trump travelled to Mexico to meet with President Ernesto Pena Nieto.
Treasury ministry spokeswoman Claudia Algorri said that Mr Videgaray presented his resignation to Mr Pena Nieto today.
Ms Algorri gave no reason for the resignation, but it came in the wake of Mr Pena Nieto's widely criticised meeting with the Republican presidential candidate in the Mexican capital last week.
The president's office announced earlier on Wednesday that Mr Pena Nieto would have a message later in the day about a change in his government.
Mr Pena Nieto has faced criticism after Mr Trump's brief visit, with many Mexicans complaining that the president was poorly advised by the people around him.
While some local media have said the visit was Mr Videgaray's idea, Mr Pena Nieto denied that in recent days and said the initiative was all his.
Mr Pena Nieto also has been ridiculed for not confronting him more directly about comments calling migrants from Mexico criminals, drug-runners and "rapists", and Mr Trump's vows to build a border wall and force Mexico to pay for it.
The wall proposal has been criticised widely and fiercely in Mexico.
Speaking at a town hall late on Thursday where he fielded questions from young people, Mr Pena Nieto sought to defend his decision to invite Mr Trump to visit.
He said the easier path would have been to "cross my arms" and do nothing in response to Mr Trump's "affronts, insults and humiliations", but he believed it necessary to open a "space for dialogue" to stress the importance of the US-Mexico relationship.
"What is a fact is that in the face of candidate Trump's postures and positions, which clearly represent a threat to the future of Mexico, it was necessary to talk," Mr Pena Nieto said hours after his annual state-of-the-nation report was delivered to congress. "It was necessary to make him feel and know why Mexico does not accept his positions."
He acknowledged Mexicans' "enormous indignation" over Mr Trump's presence in the country and repeated that he told him in person Mexico would in no way pay for the proposed border wall.
Mr Pena Nieto came under fire for not responding to Mr Trump's mention of the wall during a joint news conference on August 31, something he has since sought to correct.
A day later, Mr Trump tweeted that Mexico would pay for the wall, and Mr Pena Nieto fired back his own tweet saying that would "never" happen.