Tillerson, accompanied by Homeland Security Secretary John Kelly arrived on Wednesday and are slated to hold meetings on security, immigration, trade and the border with Pena Nieto and other officials, the bulk of which take place on Thursday.
According to sources, Tillerson will attempt to smooth over tensions sparked by brash rhetoric, plans to build a border wall, and most recently the Department of Homeland Security's new immigration guidelines, NBC News reported.
The plans unveiled on Tuesday would consider almost all undocumented immigrants subject to deportation and includes sending those who enter the US illegally via the southern border back to Mexico, even if they were not from there.
Mexico's lead negotiator with the Trump administration, Foreign Minister Luis Videgaray, said on Wednesday ahead of Tillerson's arrival that there was no way Mexico would accept the new rules.
"I want to say clearly and emphatically that the government of Mexico and the Mexican people do not have to accept provisions that one government unilaterally wants to impose on the other," he told reporters at the foreign ministry.
"We also have control of our borders and we will exercise it fully," he said.
Roberto Campa, who heads the human rights department of the Interior Ministry, said the plan to deport non-Mexicans to Mexico was "hostile" and "unacceptable".
However, White House press secretary Sean Spicer on Wednesday denied that Tillerson's trip to Mexico was an effort to repair any ill will created by the new president, reports NBC News.
He described the relationship between the two countries as "phenomenal right now".
"I would argue that we have a very healthy and robust relationship with the Mexican government and Mexican officials," Spicer told reporters during the daily press briefing. "And I think they would echo that same sentiment."
Last month, a planned visit by Pena Nieto to the White House was cancelled in the wake of a fiery spat over which nation will pay for Trump's border wall.
The pair later spoke by phone after the cancellation, calling the conversation "constructive and productive".
Widespread anti-Trump protests were held in 18 cities across Mexico earlier this month. Cities in the US held a "Day Without Immigrants" protests to showcase the importance of immigrants.