Saying countries that assure religious freedom tend to be more peaceful, Obama told a bipartisan crowd "nations that do not uphold these rights sow the bitter seeds of instability and violence and extremism.
"So," he said, "freedom of religion matters to our national security."
The president said that he and his administration have raised the issue in meetings with China, Burma, and Middle East and African nations that restrict worship.
"Even as our faith sustains us, it's also clear that around the world freedom of religion is under threat," Obama said, and protecting that freedom is "a key objective of U.S. foreign policy."
The president called for the release of American missionaries who are imprisoned in North Korea and Iran. He also criticized armed conflicts involving religion, saying that "the killing of innocents is never fulfilling God's will."
Obama has spoken every year of his presidency at the National Prayer Breakfast, a bipartisan event that began in the early 1950s.