Rafael Ramirez did not say whether anyone specifically was suspected and ruled out employees of the state-owned PDVSA oil company. President Nicolas Maduro blamed the political opposition, without providing evidence.
But a former PDVSA security chief questioned Mr Ramirez's explanation, calling it speculative and saying it raised questions about why the leak was not detected.
Shortly after the August 2012 explosion at the Amuay refinery, reports emerged of faulty maintenance including dozens of accidents before the disaster.
Mr Ramirez claimed the blaze was caused by the loosening of seven bolts at a pump, releasing gas that exploded when National Guard troops stationed at the refinery started up vehicles nearby to evacuate.
He said the disaster caused £709 million in damage. It took four days to extinguish the fire and 42 people died.
Only recently has the refinery restored production to 645,000 barrels per day of crude.
Ex-PDVSA security chief Gustavo Benitez said he found it difficult to believe insurers would pay for damages caused by the disaster based on Mr Ramirez's explanation.