Mr. Morsi and his allies in the Muslim Brotherhood stood accused of a sudden turn toward authoritarianism, as they fulminated about conspiracies, steamrollered over opponents, and sent their supporters into a confrontation with protesters the night before that call; the clash left seven people dead. But Mr. Obama did not reprimand Mr. Morsi, advisers to both leaders said.

Instead, a senior Obama administration official said, the American president sought to build on a growing rapport with his Egyptian counterpart, arguing to Mr. Morsi that it was in his own interest to offer his opposition compromises, in order to build trust in his government.

“These last two weeks have been concerning, of course, but we are still waiting to see,” said another senior administration official, speaking on the condition of anonymity to avoid aggravating relations with Egypt. “One thing we can say for Morsi is he was elected, so he has some legitimacy.” He noted that Mr. Morsi was elected with 51 percent of the vote…

[B]y muting its criticism, the Obama administration shares some of the blame, said Michael Hanna, a researcher at the Century Foundation in New York and an Egyptian-American in Cairo for the vote. “Silence is acquiescence,” he said, adding about Mr. Morsi: “At some point if you are so heedless of the common good that you are ready to take the country to the brink and overlook bodies in the street, that is just not O.K.”