The rare discovery of two large underwater 'caves', found on the reef where the government plans to build an offshore wind farm, could pose a threat to the project.

The reef off Mellieħa was chosen as the site of Malta's first offshore wind farm because it is the only area of the seabed around the islands that is shallow enough to cater for today's technology.

But if the reef turns out to be unstable or hollow in some areas, it would be extremely difficult, expensive or even dangerous to drill into the seabed to install the wind turbines.

Oxford graduate and marine geologist from the University of Malta, Aaron Micallef, 29, conducted a study of the Mellieħa reef known as Sikka l-Bajda, as part of a research project.

His team carried out a five-day survey, mapping the topography of the seabed of various offshore areas in the northeast of Malta, sending sound pulses to measure the depth of the seabed.

What they found was surprising: two large perfectly circular sinkholes (or dolines). These were probably formed during an ice age, when the reef was above the sea level. The caves would have been eroded by rainwater, which is slightly acidic, flowing through cracks in the rock.

"Basically a large hole was formed underneath the rock's surface. Eventually the roof grew thin, or the pressure on the top of the roof increased, and it collapsed," Dr Micallef told The Sunday Times.

One of the caves is 240 metres wide and eight metres deep, while the other is about half the size.

"The problem is that there may be more where these came from. It is likely that along the reef there are other caves that have not yet collapsed. And this may create problems for the wind farm project."

The reef is full of fractures, probably because it is made of upper coralline limestone overlying a layer of blue clay, causing the limestone to slip along the softer clay, as happens in various parts of Malta's cliffy coast.

Dr Micallef said: "I don't want to be alarmist. For all I know these could be the only caves and we would be able to work around them. Further studies would obviously have to be carried out. But at least we know beforehand that we could encounter difficulties."

He said the two sinkholes should immediately be classified as sites of scientific importance, as was done with the same kind of cave found above sea level, namely at Maqluba and the Inland Sea.

Marine biologist Alan Deidun said that shallow dolines could provide unique habitats to sensitive shade-seeking species, especially around the walls of the 'caves', attracting rare algae and types of coral.

He said an Environmental Impact Assessment would be carried out on the site in the coming weeks to establish whether there were any other dolines in the area and to identify the least harmful areas in which wind turbines could be built.

While a wind farm could initially damage part of the reef, there were ways to minimise this, and the wind farm itself would immediately be colonised by various species.

Dr Deidun said the reef was already damaged by constant bunkering and bombing during the Second World War.

Dr Micallef said a seismic study would provide an X-ray-like idea of what lies beneath Sikka l-Bajda and help experts understand whether other caves have been eroded within the reef.

When contacted, a spokesman for the Resources Ministry said geological studies would form part of the EIA to be conducted in the coming weeks.

"Currently a number of studies are being carried out to investigate the wind resources in the area and the impact of the wind farm on ecology. The results of the studies will allow informed decisions on the viability of the offshore wind farm."

The spokesman added that "irrespective" of the depth of the reef, preliminary assessments showed that a wind farm with a capacity up to 95 megawatts was "technically possible".

Last November, Resources Minister George Pullicino warned that should the reef off Mellieħa prove to be inadequate for a wind farm, Malta would be "stuck" and would probably have to ask the EU to reconsider its expectations.

The planned 18 to 20 turbines at Sikka l-Bajda, together with the smaller farms in Baħrija and Ħal Far, would generate almost 40 per cent of the clean energy Malta needs to reach the 2020 EU-imposed targets.