Chalabi, who has been improving relations with Washington after previously falling out with the US administration, was appointed acting oil minister after the incumbent Ibrahim Bahr al-Uloum was given leave, the officials said.
Uloum told Reuters he was "intent on resigning" while aides to Chalabi, a former financier, confirmed he had been appointed acting oil minister.
"I object to the decision of putting me on leave and the mechanism by which it was done after I objected to the government's decision to raise fuel prices," Uloum said.
The change in minister comes amid what oil officials called a "crisis in the sector" due to a sabotage attack in the north and bad weather in the south, which have stopped Iraq's oil exports by land and sea.
Iraqi oil officials said they feared the country might be facing a fuel crisis after its biggest refinery, at Baiji, north of Baghdad, was shut down due to security threats. That will affect the work of other major refineries which depend on power and crude oil from Baiji.
A ministry spokesman allied to Uloum said the country was facing an impending supply crisis. "Production in the north, centre and south is about to suffocate," he said.
The son of a prominent Shia theologian, Uloum has been directing the ministry's effort to end fuel shortages triggered by sabotage and breakdowns.
Iraq increased state-controlled prices of gasoline and diesel by 200 percent earlier this month, angering Iraqis who are used to paying heavily subsidised prices.
Uloum opposed the plan and said the price rises should have been introduced gradually to satisfy both the International Monetary Fund's demand for an end to subsidies and the demands of ordinary Iraqis for cheap fuel.
The government says the price increase was necessary to stop smuggling of Iraqi oil to other countries and also to discourage the black market inside Iraq.
Falling oil exports and fuel shortages, especially of gasoline, have raised the level of popular frustration with successive Iraqi governments since Saddam's rule.
Iraqis queuing at gasoline stations in Baghdad said they feared the Baiji closure would make their lives even more miserable.
"This will cause crises in streets and around gas stations, it will make the queuing hours even longer," said Kifah Majid, 29, a gas station worker in Baghdad.
South Iraq's oil exports, which constitute the bulk of the country's production, remained shut on Friday due to logistics problems at the Basra terminal in the Gulf.
A regional shipper said tug boats at the terminal broke down a few days ago and were undergoing repair, adding that no tankers had been loading from Basra for about a week. Bad weather, which has now cleared, also contributed to the halt.
Shipping data showed the tanker Queen Way still sitting at Basra's berth number one although it finished loading one million barrels of crude oil on December 25.
The tanker Kos was also waiting for a tug boat at Berth number three. It finished loading two million barrels on December 20.