In a tense, 43-minute phone call on Friday morning, Secretary of State Hillary Rodham Clinton told Prime Minister Benjamin Netanyahu that Israel’s plan for new housing units for Jews in East Jerusalem sent a “deeply negative signal” about Israeli-American relations, and not just because it spoiled a visit by Vice President Joseph R. Biden Jr.

Mr. Biden, in Israel this week to declare American support for its security, had already condemned the move as undermining the peace process. But Mrs. Clinton went a good deal further in her conversation with Mr. Netanyahu, saying it had harmed “the bilateral relationship,” according to the State Department spokesman, Philip J. Crowley.

Such blunt language toward Israel is very rare from an American administration, and several officials said Mrs. Clinton was relaying the anger of President Obama at the announcement, which was made by Israel’s Interior Ministry and which Mr. Netanyahu said caught him off guard.

The Israeli leader repeated his surprise about the plan to Mrs. Clinton, a senior official said, and apologized again for the timing. But that did not appear to mollify Mrs. Clinton, who said she “could not understand how this happened, particularly in light of the United States’ strong commitment to Israel’s security,” Mr. Crowley said.

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