Several citizens and seven NGOs have filed a judicial protest against the Lands Authority, calling on it to enforce contract conditions the db Group had agreed to to develop the former ITS site.
db Group has plans to build luxury apartments, a hotel and shopping complex at the St George's Bay site.
The contract, NGOs have said, required the developer to "restore" St George's Barracks, a Grade 2 scheduled building.
Despite this contractual obligation, the building was being demolished with only a wall and a coat of arms being retained. This was in clear breach of the contract and constituted a loss of national architectural heritage, the NGOs said.
Moreover, the contract stipulated that any discoveries of antiquarian or archaeological importance had to be notified to the competent authorities, and that the government should have certain rights over such discoveries.
Although archival research carried out by experts showed that plans of an underground Cold War bunker existed on site, there was no record of this being notified to the authorities as stipulated by the contract.
Heritage groups last week called on the Superintendence for Cultural Heritage to issue an Emergency Conservation Order to protect the previously undeclared bunker, which housed a sub-station in the 1950s, and a 1930s engine room underneath the St George Barracks.
Developer db Group denied that any excavation was being carried out on the bunker.
In their protest, the NGOs called upon the Lands Authority to enforce the contract and to preserve the country's heritage.
The seven organisations filing the protest are Din l-Art Ħelwa, Ramblers' Association, BirdLife, Friends of the Earth, Moviment Graffitti, Flimkien għal Ambjent Aħjar and the Bicycle Advocacy Group.