There have been no obvious signs of them washed up on the shore; no evidence that disease or human hand is behind a dramatic reduction in numbers of the sea mammal. But a routine survey has delivered the baffling news that 5,000 common seals have disappeared from the shores of Orkney and Shetland.

Zoologists from the University of St Andrews are so concerned about the slump in numbers of the creature loved by locals and holidaymakers alike that they are now undertaking the first complete survey of Scotland's common seal Phoca vitulina population in the hope of an explanation. The two teams of researchers, who are equipped with helicopters using military-specification thermal imaging technology, will fly for two hours each side of low tide - the time that offers the best view of seals - in an operation which, it is hoped, may shed some light on a disturbing 45 per cent reduction in the Orkney and Shetland population.

A major, catastrophic event - such as pollution or disease - has already been ruled out by the scientists. "If there had been one, we'd have had carcasses washing up and people would have seen them at the shore and noticed them," Callan Duck, the university's senior research zoologist, said yesterday.

Instead, the seals may be finding a substantial reduction in the sustenance available to them as a result of subtle changes in the food chain. The species relies for food on sand eels, the population of which has been dramatically reduced; the seabird population is another source which has been faring badly. Competition for food has also intensified because a major rise in the grey seal population.

Another possible cause of the decline is the presence of killer whales, though this probably does not account for the entire 5,000 reduction. "They've been seen with increasing regularity in the past five years," said Mr Duck. Other possible causes could be pollutants in the water - or more prosaic reasons relating to seal population cycles. "You could have something affecting reproductive performance which for some reason is reducing numbers," said Mr Duck.

Some conservationists are also concerned about laws governing the protection of seals, which allow fishermen to kill them if they believe that their equipment is at risk. "At the moment the law is a joke because fishermen can get away with whatever they want," said Ross Flett, the chairman of Orkney Seal Rescue.

The survey which revealed the reduction showed that numbers had dropped from 12,635 in 2001 to 7,277 last summer. Although the population on the west coast of Scotland is not believed to have declined and those who live on the east side of the country have only slightly reduced in numbers, the fall comes in a period of concern for the British seal population. The once-thriving population at The Wash, in Norfolk, is still low after the effects of the phocine distemper virus which devastated numbers five years ago.

The virus, which also wiped out half of Britain's seal colonies in 1988, killed a third of the estuary's seals in 2002 and last month, conservationists received reports that more than 40 seal pups had been washed up around an island off the Danish coast, with tests later showing they, too, had succumbed to distemper.

The British Divers Marine Life Rescue - an organisation set up in response to the 1988 outbreak - immediately warned that it was "very likely" that the virus would arrive in the UK this year, but there are as yet no signs that the disease has crossed this time. The failure of The Wash population's numbers to pick up since the 2002 outbreak is a mystery, since the population has revived in northern Europe, where 2,000 dead seals were found when the 2002 virus was at its most lethal.

The first of the two Scottish research teams set out from Berwick-upon-Tweed last week and is working its way around the east and north Scottish coasts, flying at around 90 knots and 700ft above the sea. The other will start this week in the Solway Firth and follow the west coast. They are due to converge in the Outer Hebrides. The thermal imagers they are equipped with can detect a seal up to two miles away, showing it as a small white speck on a sand bank or rock.

With Scotland accounting for a third of the UK's 30,000 common seal population, an explanation for the disappearance of so many of the creatures, which vary in colour from brownish black to tan or grey, each carrying a unique pattern of fine dark spots, is keenly awaited. "This common seal population is a very significant one and we are actively looking for answers," said Mr Duck.

Seal facts

There are around 30,000 common seals in the UK, making up 80 per cent of Britain's total seal population. There are up to 500,000 common seals in the world. As their name suggests, they are the most common species. They tend to stay around rocky shores and sandy beaches. They are not generally considered to be a threatened species, though their habit of staying near coastlines has brought them into conflict with fishermen.

Seals get caught in fishing nets and in the UK, Canada and Norway, it is legal to shoot seals that come near fisheries. It is illegal to commercially hunt seals, though this is known to sometimes occur. Pups can fall victim to foxes and large birds of prey.

The average common seal weighs 140kg and grows to 7ft. They eat up to 5kg worth of fish per day.

Male common seals (bulls) live for 20-25 years and females (cows) can live for 30-35 years.

They are largely grey in appearance, and each individual seal has its own unique pattern of brown spots. They have relatively large faces with large eyes.

Common seals can swim for several days across 50km to find feeding grounds, and dive for up to 10 minutes to depths of 1,500ft.