"I can confirm that they spoke," the official from Pena Nieto's office said on condition of anonymity without providing more details about the discussion.
The official, who was not authorized to speak publicly, said a statement would be issued late in the day.
The conversation was reported hours after Trump took to Twitter again to rail against Mexico.
"Mexico has taken advantage of the US for long enough," Trump said today, writing first on his personal Twitter account and then re-tweeting the message under his presidential handle.
Trump has angered Mexicans, perplexed economists and energized his nationalist political base by vowing to build a wall along the US frontier -- and then somehow to make Mexico pay for it.
His insistence on this point caused Pena Nieto -- who had voiced optimism that he could have good relations with Trump after the US election -- to cancel a planned visit to Washington next week.
Economy Minister Ildefonso Guajardo, who met with US officials in Washington this week, told the Televisa network that the two sides were "at an impasse."
Analysts say the spat has created the biggest diplomat rift since a drug cartel tortured and killed a US undercover agent in 1985.
Mexico's leaders have repeatedly said their country will never pay for the 3,200-kilometer border barrier that Trump says is needed to stop illegal immigrants and drug smugglers coming over.
Trump's response has been to ask the US Congress to find between USD 12 billion and USD 15 billion for construction and to help him find a way to recoup the money with some kind of tariff on Mexican imports.
Today, for example, senior aide Kellyanne Conway told CBS television that a five to 20 per cent tax may be imposed at the border.
Yesterday, White House spokesman Sean Spicer suggested that one option -- not necessarily the favored one -- would be a border adjustment tax of the kind favored by Republicans in the US Congress.
Visiting Washington yesterday, Mexico's Foreign Minister Luis Videgaray scoffed at the notion, arguing that this would just pass the cost of the wall on to US consumers of Mexican goods.
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