The temples of Hagar Qim and Mnajdra, both World Heritage sites, are currently suffering from deterioration and structural problems arising mainly from exposure to the elements. Following the recommendations of an international meeting of experts in 1999, a Scientific Committee was set up in 2000 to study the causes of this deterioration and to find ways and means to stop it. Studies carried out include environmental monitoring, thermographic measurements, further stone sampling and analysis, measurements of water runoff, and 3-D scanning of both sites and the surrounding terrain. The committee identified a number of problems namely rain, fluctuations in temperature and relative humidity, solar radiation, and pollution, including also sea salt aerosol, Sahara dust, sulphur oxide and nitrous oxide and volcanic emissions, as well as biological organisms. The committee thus proposed that the temples should be protected by temporary shelters which would provide additional time for research into the long-term preservation of the sites.

In 2003 an international competition for the design of shelters for the two temples was launched under the auspices of the International Union of Architects. The European Union through the European Regional Development Fund provided 4.2 million Euros whilst the UNESCO World Heritage Committee endorsed the project. The shelters are designed to be reversible, but also to last long enough for more research to be carried out so that a long term solution can be found. The ongoing environmental monitoring will continue when the shelters are in place, and the data obtained will be compared to data collected during the years prior to the erection of the shelters. In 2008 work started on the erection of two shelters which should last for the next 25 to 30 years, during which period work will continue on the consolidation of the temples, as well as research to identify long-term alternatives to sheltering. During the last quarter of 2008 work was carried out on the erection of the steel arches that will be support the shelter membrane. The membrane is being installed in early 2009.