WASHINGTON — President Trump delivered a brief, uncharacteristically subdued message of faith and American values to religious leaders as a fresh crisis swirled in his White House, declaring on Thursday morning “we praise God for how truly blessed we are to be American.”

“Faith is central to American life and to liberty,” Mr. Trump said at the annual National Prayer Breakfast, a gathering of religious leaders who have become a keystone of his political base. “Our founders invoked the creator four times in the Declaration of Independence. Our currency declares, ‘In God we trust.’”

Mr. Trump’s remarks came amid growing questions about how the White House handled allegations of domestic violence against one of the president’s closest aides.

The White House chief of staff, John F. Kelly, steadfastly defended the aide, Rob Porter, right up until Mr. Porter resigned on Wednesday. Officials now say the White House was aware of the charges against Mr. Porter, which contributed to a delay in granting him a security clearance for his post as staff secretary.