His comments come amid investigations into the alleged massacre of 24 civilians in the town of Haditha last November and claims of a military cover-up.
"I am troubled by the initial news stories," said Mr Bush at the White House, in his first public comments on the issue.
"If, in fact, laws were broken, there will be punishment," he said, adding: "Those who violated the law, if they did, will be punished."
The Bush administration earlier this week promised full public disclosure of the findings of military probes into the alleged killings.
The deaths were initially attributed to a clash with militants.
Two separate probes are currently underway by the US Defence Department, and officials have said those investigations are nearing completion.
The investigations aim to learn what happened on November 19, 2005 in Haditha and how the incident was handled by commanding officers in the military hierarchy.
There are fears that the political repercussions of this latest incident could be worse than the Abu Ghraib scandal.
Video images of the aftermath of the alleged massacre have been revealed this week.
A prominent US lawmaker and others have accused the military of trying to cover up the November incident.
Mr Bush recently referred to the Abu Ghraib scandal, which triggered outrage in the Middle East and across the Islamic world, as the biggest mistake committed by Americans in Iraq.
Marine Corporal James Crossman, who was deployed in Haditha the day the killings occurred and was injured in a bomb attack there, told CNN television in an interview that some of his fellow marines "might have got scared".
"Like, after seeing so much death and destruction, pretty soon you just become numb and really don't think about it anymore," said Mr Crossman, who suffered a broken back and pelvis, said.
Marines went on a house-to-house search after the bomb exploded injuring Mr Crossman and killing another marine.
The allegations of indiscriminate killing in Haditha threaten to damage the difficult US mission in Iraq as well as Mr Bush's attempts to rally flagging public support for the war.
The case has already been compared with the My Lai massacre during the Vietnam war, during which hundreds of civilians were killed by US soldiers, bolstering opposition to that war.
However Mr Bush said that rather than try to conceal the alleged crimes, the marines are compelled to seek justice in the case.
The president said he had discussed the matter with General Peter Pace, chairman of the Joint Chiefs of Staff.
The shooting came to light in a Time magazine report in late March which cited an Iraqi human rights group and Haditha residents.
According to the reports, after the bomb detonated, killing one marine, marines barged into a home in the Iraqi village, throwing grenades and shooting several people, including women and children, in cold blood.
The official version of events had insisted the civilians were killed in a roadside bomb.
The New York Times reported on Wednesday that death certificates show all the Iraqi victims in Haditha had gunshot wounds, mostly to the head and chest.