Five dead seals found on the north German coast were carrying the highly infectious phocine distemper virus (PDV), which has killed 2,000 seals in Sweden, Denmark and the Netherlands since May.
The fear now is that that the epidemic could reach the proportions seen in 1988, when 18,000 creatures died, decimating the seal population in northern Europe.
There is no effective way to stop the spread of the disease, which attacks the animals' respiratory systems. A vaccination programme is widely believed to be unworkable.
To slow the spread of the virus, corpses are being removed as soon as they are discovered.
German authorities have asked people living along the coast to report a dead seal as soon as they spot one.
About 20-25,000 seals which live in the Wadden Sea, a stretch of water which leads into the North Sea, are deemed to be at risk.
Improved conditions
Officials are clinging to the hope that improved conditions may give the seals a better chance of fighting off the virus than in the 1988 outbreak.
A statement for the German Environment Ministry said their standard of living had improved substantially since 1988.
"Experts say their health and their diet is good," the statement said.
"But above all, the level of pollution in the North Sea which can weaken the immune system of the animals has sharply decreased since 1998."
But the ministry also pointed that even if many seals were to die in this epidemic, the experience of 1988 showed that the population quickly replenished itself.
Britain is awaiting the results of a post-mortem examination on two seals discovered at the weekend which both displayed signs of the virus.
About 3,000 seals died in Britain during the 1988 epidemic.
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