"Their investigation will lay the facts out for everybody to see. And if there's an overcharge like we think there is we expect that money to be repaid," Bush told reporters in Washington on Friday.
In New York, Halliburton defended its work and said it welcomed a full review of its activities.
The Houston-based company denied that its Kellogg, Brown & Root (KBR) unit, which has performed engineering services for the military since World War II, overcharged the government by more than $120 million for fuel deliveries and meal services in Iraq under two contracts.
Critics of the Bush Administration say Halliburton, formerly led by Vice President Dick Cheney, has unduly benefited from its government connections.
"It is not fact that KBR has overcharged," Chairman and Chief Executive Dave Lesar said. "KBR has acted in full accordance with its fiduciary and contractual responsibilities."
Lesar, responding to Pentagon allegations of overcharging $61 million for fuel deliveries, said the Army Corps of Engineers directed Halliburton to buy and deliver fuel from Kuwait. The company sought and received bids from four suppliers and only one met Corps requirements, he said.
"KBR has acted in full accordance with its fiduciary and contractual responsibilities"
Chairman and Chief Executive, KBR
Lesar said Halliburton "only makes a few cents on the dollar" for the fuel deliveries. The company also cited an Army Corps of Engineers report that showed ongoing audits have found no signs of overcharging.
The fuel deliveries come under a contract, awarded in March with no competition, to restore Iraq's oil fields. So far the company has billed $2 billion under the contract, which has a cap of $7 billion. Halliburton receives a small portion of the costs as income.
Halliburton said it would cooperate with all government agencies.
On Thursday the Defense Department said an investigation found that Halliburton's Kellogg Brown & Root division may have overcharged the US government by more than $120 million for some activities in Iraq under two contracts.
Pentagon auditors found evidence the company overcharged by $61 million for delivering fuel purchased in Kuwait.
The company also inflated costs for serving meals to the military by $67 million, the Pentagon probers found, under a 10-year logistics contract (LOGCAP) awarded to KBR in 2001.