The Infrastructure Ministry has questioned the way in which the tenants of Casa Cassar, known as Casa Lanfreducci, treated the supposed remains of the knights found in the basement of the Valletta property.

The basement will form part of Renzo Piano’s open air theatre on the site of the Royal Opera House.

On Monday, NGO Flimkien għal Ambjent Aħjar, a major opponent of the project, issued photos showing human remains found years ago in the basement, which, it said, supported the claim the basement was a burial ground.

The pictures showed bones stored in white cardboard boxes reading “pasticceria assortita” (assorted pastries).

“Had the bones been found in the basement as claimed, they should have been protected in situ and reported to the Superintendent of Cultural Heritage as required by Maltese legislation,” the ministry said, adding no such report was known to have been made.

It turned the focus on the tenants of the property saying investigations had shown a “substantial volume of rock was cut and removed from the entire area of the basement’s floor by the tenants”.

The ministry stopped short of saying who the tenants were. However, it has been reported the basement of Casa Lanfreducci was until last month used by the Maltese Association of the Knights of the Order of St John. The building was leased for 50 years in 1991 and restored by the Order. The lease was terminated by the government.

“Any archaeological features that may have once existed in the rock bed would have therefore been irretrievably quarried away and lost during these works. Such works required a development planning application and should have been authorised by the planning authority,” the ministry said.

“It is a matter of concern that individuals – who publicly hold the photographed human bones to be ‘sacred’ and the site to be of historic and archaeological importance – should have handled the alleged burial ground in such an amateurish and disrespectful manner during their tenancy of the property.”

The FAA’s claim that the remains probably belonged to Knights of the Order of St John was backed by forensic expert Anthony Abela Medici who had examined the site when they were found and agrees the ministry’s plans are “shameful”.

Meanwhile, archaeological and site reports were taking place, the government said and the human remains would be “appropriately investigated” and after that given a proper burial.

The Labour Party planning and housing spokesman, Roderick Galdes called for an inquiry into the removal of the human remains and for the planning application to be withdrawn, saying the government “could not be trusted in similar projects”.