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"I was shocked and deeply saddened to hear the news from Camp Victory this morning, and my heart goes out to the families and friends of all the service members involved in this horrible tragedy," said Obama in a statement.
The Pentagon confirmed earlier the day that five U.S. soldiers were killed in a shooting incident at the U.S. base near Baghdad International airport.
Without providing further details, the military said that the case "is under investigation and more information will be released when it becomes available."
Obama assured that the government is "doing everything" it can to ensure "our men and women in uniform are protected as they serve our country so capably and courageously in harm's way."
He also said that he has met with Defense Secretary Robert Gates to get a briefing on the situation.
At the Pentagon, Gates called the incident shocking, saying "we're still in the process of gathering information on exactly what happened."
Adm. Mike Mullen, chairman of the Joint Chiefs of Staff, said "the tragedy occurred in a place where individuals were seeking help."
He also said that the incident underscores the need to allow the U.S. troops to spend more time at home between combat deployments.
The latest deaths bring the number of U.S. soldiers killed in Iraq to about 4,292 since the Iraq war broke out in March 2003.