Petronas has been one of a few non-Chinese oil companies providing gasoline to Iran, the world's fifth-largest crude oil exporter.
On Thursday, Najib was reported as saying that Petronas had decided to suspend gasoline supplies to Iran and as warning that Tehran was close to facing new international sanctions over its controversial nuclear programme.
"It is not correct. It was not a decision taken by Petronas per se. It involved a spot sale and there was no requirement anymore, so they don't do it," he was quoted as saying by state news agency Bernama on Saturday.
"It is a third party deal that was done in mid-March, not now," he added.
The national oil company said in a statement Saturday that its subsidiary had last shipped gasoline to Iran in March, but did not elaborate.
"Petronas, through its subsidiary Petronas Trading Company (PETCO), sold spot volumes of gasoline from third party traders and suppliers to customers in Iran," it said in the statement.
"The last shipment of gasoline into Iran was made in mid-March this year. PETCO's decisions in these sales were based purely on commercial considerations," it added.
Najib said on Thursday that additional sanctions on Iran over its nuclear programme were "going to be quite inevitable… unless there is some movement in the right direction by Iran."
The United States and its allies believe Iran is covertly working on a nuclear weapon, which Tehran has denied, saying it is pursuing only civilian nuclear power.
A member of the OPEC cartel, Iran has seen investment in petroleum refineries shrink as a result of US sanctions and has thus resorted to importing about 40 percent of its gasoline needs.
