Pope Francis in Chile urged peace and denounced the use of violence in the struggle for indigenous rights yesterday, while celebrating Mass just hours after fresh attacks on churches in the region.

The Pope was highlighting the conflict between the state and the Mapuche people, who centuries ago controlled vast areas of Chile but have since been marginalised.

'You cannot assert yourself by destroying others, because this only leads to more violence and division,' said the Pope, speaking in front of thousands of faithful at an airfield in Temuco, the capital of the southern Araucania region.

'Violence begets violence, destruction increases fragmentation and separation. Violence eventually makes a most just cause into a lie,' Francis warned, according to AFP.

The Pope was speaking just hours after unidentified assailants hurled incendiary devices at three Catholic churches and an evangelical church in pre-dawn attacks yesterday in the Araucania region.

The attacks came after at least five other churches had been hit by arsonists in Chile's capital of Santiago ahead of the Pope's visit.

Pope Francis himself was struck by what appears to have been an item of clothing or a towel as he greeted crowds from the popemobile on his way to an open-air Mass in Chile's capital, Santiago.

The 81-year old was hit on the left side of his face, but appeared to be unharmed, and maintained a smile as he waved to worshipers as though nothing had happened. 

In other violence, a forestry company helicopter was torched during the night, according to authorities, and a policeman was shot and wounded by a group of hooded assailants.

The aim of the violence was to 'cause disorder or disturbance of the public order' during the papal visit to Temuco, said the Chilean police chief Bruno Villalobos.

When the Pope was in Santiago, he faced protests over the Church's handling of clergy sexual abuse.

But in Temuco the papal spotlight turned to the Mapuche, who account for seven per cent of Chile's population but hold five per cent of their ancestral lands.

After the Mass, the Pope met with a group of indigenous people before returning to Santiago, where he met with youth groups at the Maipu shrine outside the city.

Thousands waited from the early hours of yesterday at the Maquehue airfield to hear Pope Francis, who dedicated the mass to the victims of human rights abuses during the 1973-1990 dictatorship of Augusto Pinochet.

The Pope said he chose to celebrate mass at the airfield because of its history as a detention centre during the military regime.

He said: 'This celebration we offer for all who suffered and died and for those who each day carry on their backs the weight of so many injustices.'

Jessica Pinto, who drove for more than three hours to see Pope Francis, told AFP: 'I think it was worth it because for a long time in this country we have needed to hear the message that Pope Francis is bringing.'