By MARK LANDLER
WASHINGTON - It was only one paragraph buried deep in the most plain-vanilla kind of diplomatic document, 40 pages of dry language committing 189 nations to a world free of nuclear weapons. But it has become the latest source of friction between Israel and the United States in a relationship that has lurched from crisis to crisis over the last few months.
At a meeting to review the Nuclear Nonproliferation Treaty in May, the United States yielded to demands by Arab nations that the final document urge Israel to sign the treaty - a way of spotlighting its historically undeclared nuclear weapons.
Israel believed it had assurances from the Obama administration that it would reject efforts to include such a reference, an Israeli official said, and it saw this as another sign of unreliability by its most important ally. In a recent visit to Washington, Israel's defense minister, Ehud Barak, raised the issue in meetings with senior American officials.
With Prime Minister Benjamin Netanyahu scheduled to meet President Obama on Tuesday at the White House, the flap may introduce a discordant note into a meeting that both sides are eager to portray as a chance for Israel and the United States to turn the page after a rocky period.
Other things have changed notably for the better in American-Israeli relations since Mr. Netanyahu called off his last visit to the White House to rush home to deal with the crisis after Israel's deadly attack on a humanitarian aid flotilla sailing to Gaza in late May. His agreement to ease the land blockade on Gaza, which came at the request of the United States, has helped thaw the chill between the governments, American and Israeli officials said.
Meanwhile, the raft of new sanctions against Iran over its nuclear program, after the passage of the United Nations resolution, has reassured Israelis, who viewed Mr. Obama's attempts to engage Iran with unease. Mr. Obama signed the American sanctions into law on Thursday.
"The overall tone is more of a feel-good visit than we've seen in the past," said David Makovsky, director of the Project on the Middle East Peace Process at the Washington Institute for Near East Policy. "It has been more focused on making sure that the Ides of March have passed."
He was referring to the dispute during a visit to Israel by Vice President Joseph R. Biden Jr. in March, when Israel approved plans for Jewish housing in East Jerusalem. Mr. Obama was enraged by what he perceived as a slight to Mr. Biden, and when Mr. Netanyahu visited a few weeks later, the While House showed its displeasure by banning cameras from recording the visit.
But despite the better atmospherics, some analysts said the nuclear nonproliferation issue symbolizes why Israel remains insecure about the intentions of the Obama administration. In addition to singling out Israel, the document, which has captured relatively little public attention, calls for a regional conference in 2012 to lay the groundwork for a nuclear-free zone in the Middle East. Israel, whose nuclear arsenal is one of the world's worst-kept secrets, would be on the hot seat at such a meeting.
At the last review conference, in 2005, the Bush administration refused to go along with any references to Israel, one of several reasons the meeting ended in acrimony, without any statement.
This time, Israel believed the Obama administration would again take up its cause. As a non-signatory to the treaty, Israel did not attend the meeting. But American officials consulted the Israelis on a text in advance, which they found acceptable, a person familiar with those discussions said. That deepened their surprise at the end.
Administration officials said the United States negotiated for months with Egypt, on behalf of the Arab states, to leave out the reference to Israel. While the United States supports the goal of a nuclear-free Middle East, it stipulated that any conference would be only a discussion, not the beginning of a negotiation to compel Israel to sign on to the treaty.
The United States practices a policy of ambiguity with respect to Israel's nuclear stockpile, neither publicly discussing it nor forcing the Israeli government to acknowledge its existence.
The United States, recognizing that the document would upset the Israelis, sought to distance itself even as it signed it.
In a statement released after the conference ended, the national security adviser, Gen. James L. Jones, said, "The United States deplores the decision to single out Israel in the Middle East section of the NPT document." He said it was "equally deplorable" that the document did not single out Iran for its nuclear ambitions. Any conference on a nuclear-free Middle East, General Jones said, could only come after Israel and its neighbors had made peace.
The United States, American officials said, faced a hard choice: refusing to compromise with the Arab states on Israel would have sunk the entire review conference. Given the emphasis Mr. Obama has placed on nonproliferation, the United States could not accept such an outcome.
It also would complicate the administration's attempts to build bridges to the Arab world, an effort that is at the heart of some of the disagreements between the United States and Israel.
Mr. Netanyahu and Mr. Obama will have plenty of other things to discuss this week. After several rounds of indirect talks, brokered by the administration's special envoy, George J. Mitchell, the United States is pushing the Israelis and the Palestinians to begin direct negotiations.
A central question, analysts said, is whether Mr. Netanyahu will extend Israel's self-imposed moratorium on new residential construction in West Bank settlements, which expires in September. He is unlikely to take such a step unless the Palestinians agree to face-to-face talks, they said.
For Mr. Obama and Mr. Netanyahu, the most basic priority may be establishing trust between them - which is why the flap over the nuclear conference, though small, is potentially troublesome.
"Most American presidents who end up being successful on Israel manage to create, even amid great mistrust and suspicion, a pretty good working relationship," said Aaron David Miller, a longtime Middle East peace negotiator. "This has been a real crisis of confidence, which cuts to the core of how each leader sees his respective world."
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