Thousands of Brazilians mobbed the Pope's car after his driver went the wrong way down a street in Rio de Janeiro.
Rio transportation secretary Carlos Osorio said the Fiat that Francis was riding in from the airport to the city centre turned into the wrong side of the 12-lane Avenida Presidente Vargas.
Instead of taking the left lanes that were free of traffic, the car turned into the right lanes cluttered with buses and taxis, forcing the pontiff's car to stop, he said.
Thousands who had lined the streets then rushed the car, reaching into the Pope's open window, many taking photos of him.
Vatican spokesman the Reverend Federico Lombardi acknowledged that the Pope's motorcade took a wrong turn, but said the pontiff was never concerned for his safety, even if his secretary, who was sitting with him in the car, was.
"His secretary was afraid, but the Pope was happy, with his hand out the window waving," Rev Lombardi said.
"There are no concerns for security. The concerns are that the enthusiasm is so great that it's difficult to respond to so much enthusiasm for the Pope. But there is no fear and no concern."
Pope Francis, the head of the Roman Catholic Church, who is on a seven-day trip to his home continent, then switched to an open-air Popemobile as he toured the main streets in central Rio.
At the official welcoming ceremony, Pope Francis said he had come "to meet young people from all over the world" attracted by the messages of Jesus.
During his stay, the 76-year-old will meet young Catholics gathering for the Church's World Youth Festival in Rio.
More than one million people are expected to pack the white sands of Copacabana for ceremonies presided over by Pope Francis. He will also visit a tiny chapel in a slum and make a side trip to venerate Brazil's patron saint, Our Lady of Aparecida.
The Pope will be hoping his visit will galvanise support for the Roman Catholic Church in Brazil.
In 1970 some 90% of Brazilians identified themselves as Catholic, but a poll at the weekend suggested that number was now down to 57%, with an increasing number of people joining evangelical groups.
Police and anti-government protesters earlier clashed outside the palace hosting the Pope's welcoming ceremony.
About an hour after the Pope concluded his short speech, police began cracking down on the protests, firing rubber bullets in an effort to disperse the crowd.
The protests, the latest in a series of demonstations in Brazil over the past few weeks, focused on government corruption and the cost of Pope Francis' visit, said to be in the region of £33m.