Pope Francis has encountered more joyous crowds in Brazil, kissing babies and greeting smitten nuns as he continued his seven-day visit.

Pope Francis has made a habit of kissing babies on his first foreign trip as pope, and he held up an official motorcade to kiss a few more.

The pontiff was in the city of Aparecida to celebrate his first public mass since arriving on Monday, followed by lunch with seminarians and bishops.

Afterwards, while riding in an open-air vehicle to catch a flight back to Rio de Janeiro, Pope Francis halted the motorcade and descended to the street.

He went to a chest-high metal barricade, greeted a crowd and kissed a baby handed his way. He then went to the other side of the road and kissed another toddler held aloft by a crowd of people.

About 40 nuns also lost their composure when they greeted Pope Francis after he celebrated mass at the Basilica of the Shrine of Our Lady of Aparecida.

Vatican spokesman the Rev Federico Lombardi said it was one "one of the most remarkable things" of Pope Francis's first full day in Brazil.

He said one nun rushed Pope Francis in a courtyard, embraced him and asked to take a photo with the pontiff. That encouraged the rest of the nuns who ran up to Pope Francis to follow suit.

Tens of thousands of faithful had flocked to the tiny town of Aparecida, tucked into an agricultural region halfway between Rio de Janeiro and Sao Paulo, braving cold winds to camp out overnight in a queue that snaked around the basilica.

Earlier in the week frenzied crowds mobbed the car carrying Pope Francis when he returned to his home continent for the first time as pontiff.

Ecstatic believers swarmed around the closed Fiat several times when it was forced to stop by heavy traffic on the drive from the airport to an official opening ceremony in Rio's centre.

Security during Pope Francis's visit has been a worry for Brazilian authorities because of his insistence on having contact with the faithful.

The Defence Ministry said four navy ships will watch over Copacabana beach when Pope Francis takes part in a Way of the Cross procession on Friday.

The ships will cruise the length of the famed beach checking boats near where Pope Francis will take part in the procession with an expected one million faithful.

A ministry statement said the security plan includes four other ships and 22 smaller boats to watch the beaches of Rio de Janeiro state during the pontiff's visit.

The pope is in Brazil until Sunday for the Catholic Church's World Youth Day festival.