A group of Palestinians descended from 15 of Jerusalem's oldest Arab families lodged a protest with the UN today in a fresh effort to prevent the construction of a "Museum of Tolerance" on the site of an ancient Muslim cemetery.

The project, run by the Simon Wiesenthal Centre in Los Angeles, has been dogged by controversy since its launch in 2004. Islamic groups and individual Palestinians complained that the site, in west Jerusalem, was the ancient cemetery of Ma'man Allah, also known as Mamilla, which housed thousands of graves dating back hundreds of years and where even today there are still many gravestones and tombs.

The Simon Wiesenthal Centre argued the site was adjacent to the cemetery and that construction would be on what is today a municipal car park.

After legal battles, the Israeli Supreme Court ruled in October 2008 that building could go ahead. But the Israel Antiquities Authority's chief excavator for the site, Gideon Suleimani, found the site was a cemetery in use for the past 1,000 years that "abounded with graves" and should not be open to construction without a full excavation, which never happened. He said his assessment was ignored by the court. Then late last year Frank Gehry, the celebrity architect working on the project, withdrew.

Some 60 Palestinians have signed a petition which was lodged today in Geneva with several UN bodies, including the high commissioner for human rights, the special rapporteur on freedom of religion and belief and Unesco, the United Nations Educational, Scientific and Cultural Organisation. "This construction project has resulted in the undignified disinterment and disposal of several hundred graves and human remains, the exact amount and whereabouts of which are currently unknown and threatens to erect a monument to 'Human Dignity' and 'Tolerance' atop thousands more graves," the petition says.

It describes the project as a violation of international human rights law and calls for a halt to construction, the reburial of all the remains and the preservation of the cemetery as a protected site.

"This tolerance museum to us is a museum of intolerance," said Dyala Husseini, who has ancestors from her family and her husband's family buried in the cemetery. "It is very inhumane, it is very humiliating and it ignores our existence as Palestinian families here in Jerusalem. Our families are here in Jerusalem and have been here for centuries," she said.

Jamal Nusseibeh said one of his ancestors, the former governor of Jerusalem Burhan al-Din al-Khazraji ibn Nusseibeh, was buried in the cemetery in 1432. "It is part of the rich fabric of Jerusalem which always has been a symbol of tolerance," he said. "The fact that anybody could wish to wipe out such a structural part of this fabric in order somehow to promote tolerance is very hard to understand."

Last month Rabbi Marvin Hier, the Simon Wiesenthal Centre's founder, said the project was on a "fantastic site in the heart of Jerusalem" and would bring "to Jerusalem and the people of Israel, a project of crucial significance to its future".

The centre has said the museum is being built on a car park next to the cemetery and that there was no protest about the construction of the car park 50 years ago. "Is it better to let this site remain a parking lot, or build a centre for human dignity there, which would teach young people mutual respect and social responsibility?" it said after the Israeli Supreme Court ruled in its favour.

The petition contains maps, photographs and other documents to make the case that the museum site is on the grounds of the cemetery, as is the car park. When the car park was built in the early 1960s there were protests, the petition says, but Palestinians in Israel were under military law, which severely curtailed their civil rights, including their ability to challenge the work.