A complaint has been submitted to State Comptroller Micha Lindenstrauss against the planned Museum of Tolerance, following a Haaretz investigation into the handling of Muslim graves unearthed at the museum's Jerusalem construction site.

The complaint was filed by attorney Kais Nasser on behalf of a new organization, the Association for Muslim Affairs, that represents the heads of various Muslim communities in Israel.

The Haaretz probe, published a month ago, revealed serious flaws in the way remains were removed from the building site, part of which is located on a former Muslim cemetery. Workers at the site said the hasty removals, sometimes carried out amid rain and mud, had resulted in damage to some of the skeletons.

Nasser asked Lindenstrauss to investigate both the way the remains were removed and the way the land was allocated to the Wiesenthal Center - which is building the museum - by the Israel Lands Administration and the Jerusalem municipality.

He also asked Lindenstrauss to examine the role played by Ehud Olmert, who was mayor of Jerusalem and then a cabinet minister with responsibility for the ILA during the relevant period. Nasser argued that since Olmert traveled overseas at the Wiesenthal Center's expense during this time, he may have had a conflict of interests.

Nasser charged that the hasty removal of the remains violated a High Court of Justice order to carry out the work in a way that minimized damage to the graves. He also argued that the person in charge of the excavation, Dr. Alon Shavit, has a conflict of interests, as he is both an adviser to the Wiesenthal Center on the project and, as an archaeologist licensed by the Israel Antiquities Authority, a representative of the state.

The Wiesenthal Center, the antiquities authority and Shavit all denied the allegations made in the Haaretz probe, saying the removal of the remains was carried out according to the highest professional standards and with proper respect for the dignity of the dead.

The Wiesenthal Center also noted that the museum is not being built on an active cemetery, but on a site that served as a parking lot for the last several decades.

In addition, Shavit rejected the allegation that he had a conflict of interests, and associates of Olmert's similarly rejected the claim that Olmert had such a conflict.

Click here to read the Museum of Tolerance Special Report on Haaretz.com