JERUSALEM - The Museum of Tolerance started off with good intentions, over $100 million in donations, an eye-catching design by architect Frank Gehry, a 2004 kickoff ceremony attended by Arnold Schwarzenegger, and a great piece of Jerusalem real estate.

But underneath that real estate, it turned out, there were Muslim graves. As a result, instead of bringing this contentious city's warring tribes together, the museum has sparked a fight with political, religious and historical dimensions between Muslims and Jews — and all this before it has even been built.

Months of arbitration have ended in deadlock, the site is enclosed in aluminum walls, and the dispute is now before Israel's Supreme Court. Even if the court gives the go-ahead, however, the Museum of Tolerance could well remain permanently tainted by allegations of intolerance.

The museum was conceived by the Simon Wiesenthal Center, a nonprofit Jewish human rights group based in Los Angeles. It was to promote coexistence in a city holy to Muslims, Jews and Christians, and claimed by both Israelis and Palestinians as a capital.

The center's plan includes a conference center, a theater, and museums for adults and children with exhibits covering Jewish history and Israel's relations with its Arab neighbors.

The Jerusalem municipality gave the Wiesenthal Center a municipal parking lot in central Jerusalem on which to build the museum.

But in Jerusalem, a parking lot is rarely just a parking lot. Before it was turned into a four-story underground garage in the 1970s, the land had been a small part of a sprawling Muslim cemetery.

The cemetery fell out of use after the creation of Israel in 1948, but many of its graves are still visible, crumbling among trees in what has become the heart of the Jewish side of the city. Part of the cemetery is now known as Independence Park. Another part had been sold much earlier, in the 1930s, at the initiative of the top Muslim clergyman of Jerusalem, to become the renowned Palace Hotel.

The project's backers say they didn't know the lot contained graves when they got it, and cite the Palace Hotel precedent and a 1964 ruling by a top Muslim cleric permitting construction on the land. But this has not mollified critics, who charge that nothing justifies the desecration of graves.

When surveyors found human remains at the site early this year, two Israeli Arab groups got a court order freezing construction.

One of the groups fighting the museum is the Al-Aqsa Company, affiliated with Israel's Islamic Movement, a rising political force among the country's 1.2 million Arab citizens.

"Islamic law is very clear: You can't build on land that was once a cemetery," said Muhammad Suleiman, a lawyer for the group. The cleric who issued the 1964 ruling was corrupt, Suleiman charged, and the fact that Arabs were silent about the parking lot's presence for decades doesn't mean they should remain silent now.

The Wiesenthal Center's compromise proposal — to move the graves, construct a memorial and fund the rehabilitation of the remaining gravestones nearby — is not good enough, Suleiman said, insisting that the museum must be moved.

The Wiesenthal Center refuses, saying it has already spent millions. Rabbi Marvin Hier, who heads the center and conceived the museum idea, said the delays alone have cost more than $1 million.

The Israel Antiquities Authority said it's impossible to cease construction every time graves are found, because it happens so often; Israel has more archaeological sites per square mile than anywhere else in the world. Often, when construction turns up Jewish graves, it is Orthodox Jews who protest and disrupt the work. Typically the problem is solved by raising the road or slightly altering its route.

"If people want to live in a country with roads and buildings, there is no choice but to build on graves," said Antiquities Authority spokeswoman Osnat Gouez.

But this museum is different, said Daniel Seidemann, an attorney active on issues affecting Jerusalem Arabs, because "The idea of having a Museum of Tolerance that is intolerant of others is problematic."

Some believe the Islamic Movement is using the affair to gain an Arab toehold in Jewish west Jerusalem. "They're not just talking about the museum," Hier said. "What they want is the whole area, all of Independence Park as well. They want to reclaim a piece of west Jerusalem."

It's a struggle over historical memory, said Yitzhak Reiter, an expert on modern Islamic history at the Jerusalem Institute for Israel Studies.

"This is mixed up with political aspirations on the part of both Islamists and Arab nationalists to return the landscape to the way it was before 1948," he said, noting that more than 400 Arab villages vanished in the fighting that accompanied Israel's creation that year. "In their eyes, Israel erased the Arab and Muslim character of the land and replaced it with one that was Israeli, and they want to change it back."

Al-Aqsa's Suleiman rejected this analysis. "This is 100 percent a question of religion," he said.

He and the museum's other Muslim opponents have found unexpected allies: Ultra-Orthodox Jews, who aren't known for their sympathy for Arab causes but who care about preserving graves.

"The desecration of the graves of people of any faith can't be justified," said Meir Porush, an Orthodox legislator. "The dead have the right to remain undisturbed."