Assadollah Gholizadeh told ISNA news agency on Monday that officials are working to tackle the software problem.
Gholizadeh also asserted there are no shortages of supply and advised motor vehicle users not to go to gas stations for a few hours if they do not urgently need to refuel.
He also dismissed reports that there disruption is a prelude to an increase in fuel prices.
Iranian Deputy Oil Minister Jalil Salari also assured the problem will be resolved within hours.
Unconfirmed reports say petrol stations have been disrupted due to a cyber attack.
Officials have not yet commented on the claim.