Officials said the Jakarta-based council will be a body similar to that of OPEC for oil producers.
Indonesian Resources Minister Rizal Ramli said the council will be a "game changer" for an industry under pressure from falling prices and unsustainable farming practices.
The two countries account for 85 per cent of the world's palm oil production, and the plunge in prices have hurt their economies.
"It will be a game changer for the palm oil industry in many ways," Rizal said after a signing ceremony to establish the council.
Malaysian Plantation, Industries and Commodities Minister Amar Douglas Unggah Embas said the council will not fix the price of palm oil, but will seek to ensure a sustainable price by organising and harmonising stock management.
Rizal said the council will develop a framework for sustainable palm oil. By pushing for high standards of sustainable farming, he said it will help to prevent the burning of forests to clear land for agriculture in Indonesia that has caused a thick dusty haze across the region every year.
"We know we still have to work hard to minimise the impact" of haze, he said.
The two countries will each contribute $5 million to the council's operations and operational details are still being ironed out, officials said.
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