“Let’s cut the family fighting,” said Senator Joseph I. Lieberman, independent of Connecticut. “It’s unnecessary; it’s destructive of our shared national interest. It’s time to lower voices, to get over the family feud between the U.S. and Israel. It just doesn’t serve anybody’s interests but our enemies’.”

Relations between Israel and the United States have been uneasy ever since Mr. Obama took office with a plan to rekindle the peace process by coupling a demand for a full freeze in Jewish settlement construction with reciprocal confidence-building gestures by Arab countries.

Neither happened, and Mr. Obama, who is not as popular in Israel as he is elsewhere around the world, was forced last September to make do with Mr. Netanyahu’s offer of a 10-month partial moratorium on settlements in the West Bank. But the president was outraged by the announcement of 1,600 housing units in an ultra-Orthodox neighborhood in East Jerusalem during Mr. Biden’s visit, administration officials said.

Mr. Obama was deeply involved in the strategy and planning for Mr. Biden’s visit and orchestrated the response from Mr. Biden and Mrs. Clinton after it went awry, these officials said.

The administration has used language intended to telegraph anger, defining the dispute not only in terms of the damage it could cause to the peace process but to the American relationship with Israel.

“That is a whole different order of magnitude of importance,” said Daniel Levy, a former peace negotiator who is senior fellow and head of the Middle East Initiative at the New America Foundation, a research group.

The last time relations between the United States and Israel became this strained, analysts said, was when James A. Baker, then secretary of state, clashed with the Israeli government in the early 1990s, also over settlement policy. The United States ended up withholding loan guarantees from Israel for a time.