Pope Francis ended his tour of Chile and Peru with an open air Mass for more than 1 million people on Sunday, after a tour dogged by a backlash over what many see as his insufficient resolve to tackle sexual abuse in the Church.

In the final hours of his six-day visit to the two nations, Francis warned in improvised remarks that Latin America was in a deep crisis from corruption scandals, with politics in most countries 'more sick than well'.

'Politics is in crisis, very much in crisis in Latin America,' he said, pointing to construction company Odebrecht, which has admitted to paying billions in bribes, as an example of greed run amok across the continent of his birth.

The Catholic Church's record on sexual abuse loomed large in both countries, but mostly in Chile, where Francis sparked outrage by saying criticism of a bishop he appointed who is accused of protecting a paedophile was 'all slander'.

Francis told reporters in Chile there was no evidence against the bishop, spurring Cardinal Sean O'Malley of Boston to sympathise with victims who were pained by the pope's comments in an unusually blunt statement.

O'Malley, a top adviser, was also in Peru for the trip and celebrated Mass with Francis at Las Palmas Air Base just before the pope was due to leave for Rome.

Despite the estimated 1.3 million attendance in Lima, the Church is losing followers in Latin America. Even before the pope's off-the-cuff remarks in Chile, a poll by Santiago-based think tank Latinobarometer showed the number of Chileans calling themselves Catholic had plummeted to 45 per cent from 74 per cent in 1995.

The number of Catholics in Peru, where Francis consistently had a more enthusiastic reception, remains high at around 72 per cent, according to a Datum poll, though it has fallen in the past decade.

'Francis here there is proof!' read a banner hanging from a Lima apartment with a picture of Luis Figari, the founder of an elite Catholic society who is scheduled to go on trial in Peru this year for sexual abuse of minors. Figari has denied wrongdoing.

Francis ordered the Vatican to appoint an administrator to run the society, Sodalitium Christianae Vitae, a week before his trip.

As the first pope to visit the Amazon in more than 30 years, Francis made a ringing defence of indigenous people and the environment on Friday, saying big business and 'consumerist greed' could not be allowed to destroy a natural habitat vital for the entire planet.

He extended his condemnation of greed to corruption, saying in an appearance beside embattled Peruvian President Pedro Pablo Kuczynski that all parts of society, including the Church, needed to work to combat it.

In Peru alone, one former president has been detained for allegedly receiving bribes from Odebrecht while a warrant is out for another. Kuczynski was nearly impeached in December for not revealing that a company he used to run did business with Odebrecht. He denies wrongdoing.

Francis has previously mentioned corruption on trips to Latin America, where he has also visited Brazil, Bolivia, Ecuador, Paraguay, Mexico, Cuba and Colombia but not his native Argentina. 

In a message to clergy in Peru he urged them to laugh more and not take life too seriously. 

'I'm telling you it's hurtful to see some bishop, some priest, some nun withered, and it hurts me more to see withered seminarians,' he said. 'It's good for us to remember that our vocations are a call out of love to love, to serve, not to get something for ourselves.'

Additional reporting by Reuters.