The fire "is under control and in just a matter of hours we will extinguish it completely" with the help of 120 firefighters, said Asdrubal Chavez, vice president of Venezuela's state oil company, PDVSA, in a television interview.
The official said the lightning struck two gasoline storage tanks overnight in the El Palito refinery, in Puerto Cabello in the northern state of Carabobo.
Chavez said the fire was out in one tank and the other was still burning.
El Palito has a capacity of refining 140,000 barrels of crude oil a day, according to PDVSA's website.
Last month, a gas leak at the Amuay refinery triggered an explosion that killed 20 members of a national guard unit assigned to protect the facility, along with some members of their families.
The fire spread to three storage tanks before being brought under control three days later. The refinery, Venezuela's biggest, had resumed operations by the end of that week.
President Hugo Chavez has ordered an investigation into the cause of the massive explosion -- the worst in the history of Venezuela's oil industry -- while brushing aside accusations of declining maintenance and safety at the plant.
Venezuela has the largest oil reserves in the world. Its reserves, which the government estimates at 297.57 billion barrels, surpass those of Saudi Arabia, which has the biggest refining capacity.