The fire hit a fuel storage tank at the small Siniya refinery in Salahuddin province. There were no reports of casualties, the ministry statement said.
The fire was extinguished and operations resumed within few hours after the attack, the ministry said, citing the state-owned Northern Refining Company that runs the refinery.
The Siniya refinery is near Iraq's largest oil refinery, Baiji, which sustained major damage during the war against the Islamic State group. The refinery was overhauled and eventually reopened in 2017 following the extremist group's defeat.
It was not immediately clear who was behind Sunday's attack.
Although IS no longer holds territory in Iraq, the group maintains sleeper cells and frequently carries out attacks across parts of the country, including the north.
Iranian-supported armed groups are also believed to be behind a series of rocket and mortar attacks targeting US interests in Iraq, frustrating the Trump administration, which in September threatened to close its embassy in Baghdad if they continue.