"Six million Jews were killed, more than the entire Jewish population of Israel today. Denying that fact is baseless, ignorant, and hateful," he said.
Asked whether he was doing everything possible to stop genocide around the world so that "never again" is not just a hollow refrain, Obama explained what the phrase means to him but not what he was doing.
"On the issue of genocide, I think "never again" means that the international community has an obligation, even when it's inconvenient, to act when genocide is occurring," he said.
He focused on his administration's efforts on Darfur, where he recently dispatched a special envoy, General Scott Gration, but did not address Sri Lanka or the broader question on genocide.
Earlier today, President Obama met one-on-one with Merkel and both leaders affirmed the close relationship between the United States and Germany.
Obama said it is essential for the two nations to work together with the global community to make progress on national security, economic issues and climate change.
In their meeting, the two leaders discussed Afghanistan and Iran. Obama said the United States was committed to "serious dialogue" with Iran but it needs to be in cooperation with Germany, China, France, Russia, and the United Kingdom.
Obama said Merkel is open to discussions about Guantanamo Bay but he has not asked for hard commitments and she has not offered any, other than discussions about ways to move forward.
"I don't anticipate it's going to be resolved any time in the next two or three months," he said.
Merkel reiterated her longstanding view that Guantanamo Bay should be shut down and expressed confidence that they will find a common solution.
Right out of the gate at a press conference, Obama had to defend his schedule here after criticism in the German media about how long he was staying here and where he chose to visit. Obama chalked it up to scheduling and said there are only so many hours in the day and he has a lot to fit in on a short trip.
Later today, Obama is scheduled to visit American service members at Landstuhl Regional Medical Center.
On Saturday, Obama plans to mark the 65th anniversary of the D-Day invasion with remarks at Normandy and a tour of the American Cemetery there. The president is expected to recognize the service of American veterans who will be in the audience for his speech and underscore the sacred trust the government has to veterans.
Also on the agenda is a meeting with French President Nikolas Sarkozy and an outing with Mrs. Obama and the first daughters, who will join the president in Paris.