RIO DE JANEIRO (AFP) - Pope Francis's popularity on his Latin American home turf posed a challenge to Brazilian authorities on Tuesday after adoring crowds mobbed his car on his landmark visit to Rio de Janeiro.

The fervour that surrounded the pontiff's arrival on Monday initially wrong-footed the organisers of the trip, which began with a raucous reception from throngs of cheering pilgrims.

Despite heightened security for Latin America's first pope, legions of Roman Catholics were able to block his convoy and reach inside his car's open window.

The 76-year-old Argentine appeared delighted and waved and smiled while bodyguards struggled to keep people at bay. His secretary later admitted to being terrified, but the pope was upbeat.

"Thank you to all of you and to all the authorities for a magnificent welcome in Rio," the pope wrote on Twitter on Tuesday.

The authorities blamed the chaos on bad internal communication.

The city government said the pope's driver had taken a wrong turn, keeping the car stuck in traffic for several minutes.

The defence ministry agency in charge of security for events said the pope himself had asked the driver to slow down to greet the faithful.

"There's no need to dramatise what happened. Everything turned out well, nobody came to harm the pope," said Vatican spokesman Federico Lombardi.

The highlight of the papal trip to the world's most populous mainly Catholic country will be World Youth Day, a five-day event that kicks off on Tuesday.

The pontiff's trip, however, followed demonstrations in the country over political corruption and a failure to provide basic services.

Police on Monday used tear gas and water cannon as hundreds of protesters demonstrated against the US$53 million (S$67 million) spent on the pope's visit.

The clashes came after the pope met with President Dilma Rousseff at the Rio state governor's palace.

A policeman said they charged at demonstrators after someone threw a Molotov cocktail.

Five people were detained and an AFP photographer who was clubbed on the head by police required three stitches. Further public demonstrations are planned for Friday.

The military had earlier disclosed that troops found and destroyed a homemade explosive device in the bathroom of a parking lot at a sanctuary that the pope will visit in Sao Paulo state this week.

Pope Francis had unnerved local authorities by deciding to leave his armoured "Popemobile" behind. He sat in the back of a small four-door car to head from the airport to the city and then climbed on to an open-top jeep to greet more crowds.

"The pope's secretary told me he was terrified, but the pope kept smiling," Vatican spokesman Lombardi told reporters.

The pope has no public events scheduled for Tuesday and will spend time at a hillside private residence.

Pope Francis is bringing his social message of a "poor Church for the poor" but his mission is also to re-energise the faithful.

Even in Brazil, his flock is shrinking while Evangelical churches are growing.

Speaking alongside President Rousseff, the pope used his first day in Rio to urge young Catholics to "go and make disciples of all nations". But a poll by Datafolha Institute on Sunday showed just 57 per cent of Brazilians now call themselves Catholic, while 28 per cent say they are Pentecostal or non-Pentecostal Evangelicals.

More than 90 per cent identified as Catholic in the country's 1970 census.

World Youth Day, which is expected to attract 1.5 million people, will officially kick off Tuesday with an evening mass led by the archbishop of Rio, Orani Joao Tempesta, on the beach of Copacabana.

But the faithful will have more opportunities to get close to the pope, who has made a habit of breaking with protocol to better connect with his flock.

On Wednesday, he will visit the Shrine of Our Lady of Aparecida in Sao Paulo state, where the explosive was discovered on Sunday.

Authorities said the device was nowhere near the area the pope and pilgrims will visit. Vatican spokesman Lombardi described the explosive as "very crude" and insisted that it was no cause for concern.

Pope Francis will return to the crowds of Rio on Thursday, visiting one of the city's sprawling shantytowns before addressing his young flock on an ornate stage on Copacabana.

On Friday, he will walk the Stations of the Cross along the beach, but the Anonymous Rio protest group called for a demonstration near the site to denounce government waste.