Defense Secretary Leon Panetta has said the death penalty could be possible in the case.
Obama's message was aimed at Afghans and at Americans for whom the killings were a reminder that tens of thousands of U.S. forces are fighting in Afghanistan more than 10 years after the war began.
Obama insisted that the killings will not change U.S. commitment to finishing the job in Afghanistan, but he was clearly trying to reassure Americans that he will close out the war.
"Make no mistake, we have a strategy that will allow us to responsibly wind down this war," Obama said.
"We're steadily transitioning to the Afghans who are moving into the lead. And that's going to allow us to bring our troops home."
He repeated the timetable for bringing forces home that he had already laid out: 23,000 troops by the end of this summer, on top of 10,000 removed last year. He did not give a schedule for withdrawal of the approximately 68,000 U.S. forces that will remain in Afghanistan at the end of this year.
The U.S. and NATO allies agreed more than a year ago to leave forces in Afghanistan through 2014. There is political pressure in Europe, and increasingly in the United States, to speed up that deadline.
"There's no question that we face a difficult challenge in Afghanistan, but I am confident that we can continue the work of meeting our objectives, protecting our country and responsibly bringing this war to a close," Obama said.
More on the Afghan massacre
Delegation attacked • Taliban insurgents opened fire on two brothers of Afghan President Hamid Karzai as they left a memorial service Tuesday for 16 villagers allegedly killed by a U.S. soldier. Qayum and Shah Wali Karzai and other top Afghan officials in their delegation escaped in their cars unharmed from the ambush in the country's south. But one Afghan soldier was hit in the head almost immediately and died, while two other Afghan army personnel were wounded in the 20-minute firefight that ensued in one of the two villages in Kandahar province where the killings had occurred two days before.
Hearing for suspect • A military court held a hearing for the American soldier suspected of killing 16 Afghan civilians and found probable cause to keep him in detention, a spokesman said Tuesday. Col. Gary Kolb, a spokesman for the U.S.-led military coalition in Kabul, said Tuesday that a 48-hour probable cause assessment was completed and that the service member continued to be confined. U.S. Secretary of Defense Leon Panetta has said that the soldier could face capital punishment.