In an interview with Mexican daily Excelsior, he called Mr Trump's rhetoric "strident".
He added that "that's how [Italian fascist leader] Mussolini got in, that's how Hitler got in".
The Mexican leader also said that Mr Trump had hurt US-Mexico relations.
Donald Trump has said that if he is elected he will build a wall along the US-Mexico border to keep migrants from crossing into the US illegally.
The Republican candidate has also insisted that Mexico would pay for the border wall, which President Pena Nieto dismissed out of hand.
He said there was "no scenario" under which Mexico would ever pay for such a wall.
Mr Trump, who has made the fight against illegal immigration the main plank of his campaign, outraged Mexicans last June when he called undocumented Mexican migrants "criminals" and "rapists".
President Pena Nieto said Mr Trump offered "very easy, simple solutions to problems that are obviously not that easy to solve".
"And there have been episodes in human history, unfortunately, where these expressions of this strident rhetoric have only led to very ominous situations in the history of humanity," he said.
"That's how Mussolini got in, that's how Hitler got in, they took advantage of a situation, a problem perhaps, which humanity was going through at the time, after an economic crisis," he added.
President Pena Nieto, who had up until now avoided commenting on Mr Trump's candidacy, insisted he would be "absolutely respectful" of the US political process.
His predecessors in office, however, have been more outspoken.
Former President Vicente Fox used an expletive on live television when he said Mexico would not pay for the border wall proposed by Mr Trump.
Felipe Calderon, who governed from 2006 to 2012, also dismissed the idea saying: "Mexican people, we are not going to pay any single cent for such a stupid wall!"
Mexican President Enrique Pena Nieto has compared the rhetoric of US Republican presidential candidate Donald Trump to that of German Nazi leader Adolf Hitler.