Ecuador's President Lenin Moreno has agreed to suspend a decree that ended fuel subsidies following meeting with leaders of indigenous groups that have been organising road blocks, protests and the occupation of energy infrastructure.

United Nations mediator Arnaud Peral told reporters on Sunday that the indigenous leaders had agreed to call off the protests that have disrupted oil production at oilfields in the eastern Amazon region and forced Moreno to hold cabinet in the port city of Guayaquil.

Ecuador has subsidised gasoline and diesel prices for decades, and the decision to eliminate these benefits was part of a broader austerity package adopted after Moreno's administration availed itself of a International Monetary Fund stand-by loan.

The Moreno administration will now consult indigenous groups about the terms of a new package of measures aimed at reducing Ecuador's budget deficit.

National debt soared when ex-president Rafael Correa pursued a loose monetary policy in the face of tumbling oil prices.

"Everything must be aimed at stabilising the country and stabilising our severely-degraded budget situation. Fundamentally, our agreements must be aimed at solving problems," Moreno stated after meeting indigenous leader.