At least 53 people were also injured in the blast at the Amuay plant in Falcon State in the north-west of the country, officials announced.
State Governor Stella Lugo said nearby houses had been damaged by the blast. The fire is said to be under control.
The refinery, one of the biggest in the world, produces 645,000 barrels a day.
Ms Lugo said there was no risk of further explosions.
Among the dead is a boy of 10. The army was sent in to help ferry the injured to hospital.
Analysts say refineries in Venezuela, South America's biggest oil producer, have suffered from a long list of problems including power failures and accidents.
It was not immediately how the explosion might affect oil shipments from Venezuela.
"We are deploying our whole fire service team, all our health team, the whole contingency plan on the orders of [President Hugo] Chavez to first of all care for the people affected by this emergency," Governor Lugo said on state TV.
Energy Minister Rafael Ramirez said supplies of fuel had been cut off to the part of the refinery still burning.
Troops secured the area and were helping oil workers inspect the damage, as they looked for the cause of the leak.
Mr Ramirez said the blast had occurred at 01:11 (05:41 GMT) on Saturday.
"The gas cloud exploded, igniting at least two storage tanks and other facilities at the refinery," the energy minister told state TV.
"It was a significant explosion, there is appreciable damage to infrastructure and to houses opposite the refinery."
Venezuelan Vice-President Elias Jaua said on his Twitter account that military air ambulances had been dispatched to help evacuate the injured.
He added that the defence minister was travelling to the refinery along with Ms Ramirez and other officials.
Amuay, on the Paraguana Peninsula, is part of the Paraguana Refinery Complex, which also includes the adjacent Cardon refinery.
It is one of the biggest refinery complexes in the world with an overall capacity of 955,000 barrels per day, Reuters news agency notes.
Source: BBC News
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