Pope Francis (left) and Mexican President Enrique Pena Nieto applaud a performance at Benito Juarez International Airport in Mexico City on Friday. Photo: AFP

Pope Francis will be the first pontiff to enter Mexico's National Palace to meet the country's president on Saturday as he starts a tour that will highlight the country's violence and migration troubles.

After having arrived in Mexico City late on Friday amid thousands of Catholics who swarmed the streets to welcome him, the pontiff will hold talks with President Enrique Pena Nieto at the ornate palace in Zocalo Square.

The choice of location has symbolic significance, as none of the pope's predecessors has ever been invited there, even though heads of state are usually greeted at the palace.

While Mexico is the world's second most populous Catholic country after Brazil, its governments throughout most of the 20th century were militantly secular and had testy ties with the church. But diplomatic relations with the Vatican were restored in 1992.

The pope's presence at the National Palace "closes a cycle," said Mexican Ambassador to the Vatican Mariano Palacios Alcocer.

The meeting with the Argentine-born pontiff could also give Pena Nieto a respite from the nation's persistent problems, including a prison riot that killed 49 inmates on Thursday and the disappearance of 43 students in 2014.

"It's the Mexican president, of course, who has the most to gain from basking in the glow of one of the world's most popular figures," Andrew Chesnut, religion professor at Virginia Commonwealth University, told AFP.

Hours before arriving in Mexico, Pope Francis took care of another, much older rift by holding a historic meeting with the head of the Russian Orthodox Church, Patriarch Kirill, in Cuba in a bid to end a 1,000-year-old falling out.

After his meeting with Pena Nieto, the pope will make a pilgrimage to the Basilica of Our Lady of Guadalupe, a major Catholic shrine.

The basilica houses an image of the Virgin Mary that Catholics believe was miraculously imprinted on a piece of fabric after she appeared to an indigenous peasant in 1531.

The following days will take the pope to some of Mexico's most notoriously poor and violent regions.