At a meeting with representatives of indigenous groups at a UN agricultural meeting on Wednesday, the pope said people have the right to protect their culture and territories.
He said: "In this regard, the right to prior and informed consent should always prevail. Only then is it possible to guarantee peaceful cooperation between governing authorities and indigenous peoples, overcoming confrontation and conflict."
The pontiff added that governments need to recognise that members of indigenous communities are part of the population and must be "appreciated and consulted" in discussions which affect the whole country.
Pope Francis' reference to prior consent is enshrined in the UN Declaration on the rights of indigenous peoples, which was adopted by the UN in 2007 over the opposition of the US, Canada, Australia and New Zealand.
Pope Francis has long given his support to indigenous groups, criticising what he called a profit-at-all-cost mentality of the administration in his home country of Argentina which has negatively impacted native tribes in the region.