Francis met with representatives of indigenous peoples attending a UN agricultural meeting and said the key issue facing them is how to reconcile the right to development with protection of their cultures and territories.
"In this regard, the right to prior and informed consent should always prevail," he said. "Only then is it possible to guarantee peaceful cooperation between governing authorities and indigenous peoples, overcoming confrontation and conflict."
The tribes say the pipeline, being built by Texas-based Energy Transfer Partners, threatens their drinking water, cultural sites and ability to practice their religion, which depends on pure water.
The last piece of the pipeline is to pass under a reservoir on the Missouri River, which marks the eastern border of both tribes' reservations.
The company has insisted the water supply will be safe.
US President Donald Trump, who had long signaled his support for the pipeline, last month instructed the US Army Corps of Engineers to proceed with construction.
Francis, history's first Latin American pope, has been a keen backer of indigenous rights and has frequently spoken out about their plight.
The pipeline dispute has led to protests and clashes in recent months that have resulted in some 700 arrests.
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