Chalabi replaces Ibrahim Bahr al-Uloom, who was placed on a one-month leave, the Washington Post reported. Bahr Uloom had threatened to hand in his resignation in protest of hikes in gas prices.
There is likely to be another shakeup once a new government forms following the recent parliamentary elections.
The country's largest oil refinery has been shut down because of insurgent death threats against tanker truck drivers, and oil exports have been halted from the southern seaport of Umm Qasr.
"If these issues are not solved soon, the country will be facing an uncontrollable situation," said oil ministry spokesman Assim Jihad. "Dr. Chalabi will be here for the short term, but this will need to be solved by the new government, by the Ministry of Defense and by the coalition forces."