Pump prices for the two fuels will now be set on the basis of world prices and adjusted each month, the ministry said in a statement carried by the official WAM news agency.
The move is expected to save billions of dollars a year.
The International Monetary Fund said in a report released on Monday that the UAE has been spending USD 29 billion a year subsidising petroleum products and electricity.
Fuel prices in the UAE are already the highest of any of the six Gulf Arab states.