JERUSALEM, OCT. 17 -- As the United States and Israel face off over the refusal by the government of Prime Minister Yitzhak Shamir to accept a U.N. investigative mission, an issue that has haunted the Bush administration's Middle East diplomacy once again looms in the background: Israel's passionate but disputed claim to Jerusalem.

Shamir has refused to accept the U.N. mission, unanimously approved by the Security Council and backed by the United States, in part because of what he says is one-sided language of the U.N. resolution condemning Israeli police for the shooting of at least 19 Palestinian demonstrators during riots on the Old City's Temple Mount last week.

But Shamir's advisers and other officials here say the underlying reason for the government's stubbornness -- and the relatively strong support it has received from Israelis and American Jewish leaders -- is the belief that a U.N. mission to Jerusalem would undercut Israel's claim to the entire city as its "eternal capital."

"Jerusalem is the key," a senior Foreign Ministry official said. "It is our capital, we are sovereign here, and we simply cannot allow the United Nations to treat it as if it were occupied or disputed territory. On that there is a consensus in this country."

Diplomats with experience in the Middle East know that Israeli governments bridle at any initiative they see as diluting their claim to the Holy City. Still, Israeli officials and some American Jewish leaders say, Shamir's defiant stand in this case also can be connected to the Bush administration's past handling of the Jerusalem issue, a record that has come to be seen here as a symbol of the troubled relationship Israel has had with this American president.

"This administration is perceived as taking the U.S.-Israeli relationship in directions where it hasn't been in the last decade," said Harry Wall, the Jerusalem representative of the Anti-Defamation league of B'nai B'rith. "One of the sore points is clearly Jerusalem, and by raising it Washington may have opened a Pandora's Box."

Neither the United States nor the United Nations has ever recognized Israel's designation of Jerusalem as its capital or its annexation of the eastern, Arab neighborhoods of the city, including the ancient, walled Old City, following their capture from Jordan in 1967 after Jordan entered the war against Israel. For years, the U.S. position has been that the final status of Jerusalem -- which is holy to Christianity and Islam as well as Judaism -- can be determined only by negotiations.

Past U.S. administrations, particularly the Reagan administration, avoided the Jerusalem issue because they saw it as a potential spoiler for any diplomatic progress in the region. Unlike its occupation of the neighboring West Bank, Israel's annexation of East Jerusalem is broadly supported within this country and among American Jewish leaders and has substantial backing in Congress.

U.S. diplomatic strategy has been to postpone the question of Jerusalem's status to the distant end of any Middle East peace process, and in the last decade, American administrations have tended to overlook Israeli efforts to consolidate control of the city by building new Jewish neighborhoods on its eastern side.

In contrast, discussion of Jerusalem by Bush and Secretary of State James A. Baker III helped derail their painstaking efforts to come to terms with Shamir-led governments twice in the past eight months. In both cases, the administration has chosen to dispute Israel on the construction of Jewish housing in East Jerusalem -- a battle last fought, and lost, by the Carter administration. Since then -- in the view of some -- the issue has been sealed by the growth of Jewish population in East Jerusalem to some 120,000.

In each case, Israel's reaction to the housing conflict has spilled over into a larger and more pressing issue, poisoning the atmosphere between the two governments and undermining weeks or months of patient diplomacy.

In February, after months of work, Baker appeared on the point of winning Shamir's agreement to a formula for the first Israeli-Palestinian negotiations, a potentially important breakthrough in the regional peace process.

Then, on the day when Shamir was meeting with Likud ministers to reach a final decision, Bush publicly announced opposition to the expansion of Jewish "settlements" in East Jerusalem through the placement there of Soviet immigrants. Infuriated, Shamir used the occasion to make a point on the Jerusalem issue, and balked at a provision in the Baker plan that would have allowed the participation in negotiations of a Palestinian based in East Jerusalem.

Many political observers here and in Washington felt Shamir had merely seized on the Jerusalem issue as an excuse for rejecting the Baker plan. But the prime minister's supporters later argued that by raising the profile of the Jerusalem issue, Bush had weakened Shamir at the point at which he was already most vulnerable to attack from right-wing opponents to the peace process.

In the case of the latest U.S.-Israeli dispute, the violence on the Temple Mount, known to Arabs as Haram Sharif, occurred just as Washington and Israel were once again developing a difference over settlements in East Jerusalem.

Only six days before the riots, Baker and Foreign Minister David Levy finally reached agreement on the terms by which the United States would provide Israel with loan guarantees for $400 million for housing construction for Soviet immigrants. Levy rejected most of the conditions the U.S. sought, but agreed to write a letter saying that the government did not intend to encourage immigrants to settle beyond the "Green Line" -- a term that refers to Israel's pre-1967 border.

Within hours, it became clear that Baker and Levy understood different things by the term Green Line. For Baker, it apparently meant that Israel would not settle Soviet immigrants in East Jerusalem, since it was outside the pre-1967 Green Line. But for Levy and Shamir, the agreement did not prevent construction in East Jerusalem, since Israel felt that its annexation of East Jerusalem effectively brought it within the Green Line.

In the past 10 days, even as the controversy over the Temple Mount violence has raged, Shamir's government and the Bush administration have been engaged in a parallel war of nerves over East Jerusalem construction. First, goaded by hard-line rivals within his government, Shamir announced plans for a new Jewish neighborhood in East Jerusalem. Baker responded by publicly releasing the text of Levy's letter. Then hard-line Housing Minister Ariel Sharon announced the construction of 15,000 apartments for immigrants in Jerusalem in the next three years, most of them beyond the 1967 Green Line.

In recent days, the dispute over the housing and Israel's refusal to accept the U.N. delegation have become intertwined both in public debate and in maneuvering among rival politicians in the government. Both Levy and Shamir have been attacked by Sharon and other hard-liners for agreeing to the Green Line language and accused of "selling out" Jerusalem for U.S. loan guarantees.

As a result, Shamir, in the view of analysts here, cannot now afford to make concessions to the Security Council delegation without risking an all-out assault by the Israeli right -- a challenge he is no more ready to face than he was in February, when Baker's negotiation plan collapsed.

"When you raise the issue of Jerusalem, all the calculations here change," said Yossi Olmert, director of the Government Press Office. "And that is something the Americans need to understand."

Special correspondent Trevor Rowe reported from New York:

A U.S. official at the United Nations predicted today that a compromise solution would be reached in the dispute with Israel over the U.N. delegation and that a U.N. mission would leave for Israel by this weekend.

The official said even if the mission is not received by the Israeli government at the ministerial level, it could still meet with the Israeli Human Rights Commission and similar humanitarian groups.

On Saturday, the Council voted to condemn the Israeli action and to have Secretary General Javier Perez de Cuellar send a fact-finding mission that would report back by the end of the month. However, the Israeli government said it would not receive the mission.

U.N. Seretary General Javier Perez de Cuellar, who asked Israel's ambassador for "clarifications" to Israel's refusal to accept a delegation, told reporters today that he had gotten no answer but that Thursday was a reasonable time by which to receive a reply. "Then I will draw my own conclusions and make my own decisions," he said.

Israel's ambassador to the United Nations, Johanan Bein, has suggested that the secretary general's mission could travel to Israel as tourists, but Perez de Cuellar ruled this out, saying, "I cannot accept that they go as tourists. . . . I want them to be received with respect."

He said he also wanted Israel to provide the "necessary facilities," which he described as the ability to "move around and to observe, that they be afforded the facilities for producing a fair report of what happened."