A trawlerman on Shetland is facing jail or more than £100,000 in fines after he admitted clubbing 21 seal pups to death on a remote, uninhabited island.

James Stewart, a crewman on the Altaire, one of the UK's largest herring and mackerel trawlers, was seen by staff from Scottish Natural Heritage smashing in the seals' heads with a fence post on the island of East Linga in November last year.

Stewart, 47, from Symbister, on the fishing island of Whalsay, east of Shetland's main island, pled guilty to a charge of mutilating, beating and crushing the baby seals at Lerwick sheriff court this morning.

A not-guilty plea from his co-accused John Eunson, 44, a local ferry captain also from Symbister, Whalsay, was accepted by the crown. This case, one of the most significant in recent years, follows mounting anxiety about the scale of attacks on seals by fishermen and fish farm workers, who blame the mammals for destroying their nets and damaging fish stocks, threatening their livelihoods.

Leading supermarkets and the Royal Society for the Prevention of Cruelty to Animals promised to clamp down on seal persecution after The Guardian revealed new evidence of a sudden decline in common seal numbers UK-wide last year.

Sheriff Graeme Napier told Stewart: "I take a very serious view of the offending in this case. I can see no justification for it whatsoever." Before adjourning the case until 25 March for social inquiry and custody reports, he warned Stewart that a prison was an option he was considering, and repeatedly demanded an explanation for his action.

Under the Wild Mammals (Protection) Act 1996, each offence carries a maximum fine of £5,000, leaving Stewart liable for a possible total fine of £105,000, or six months in prison per offence.

It is also illegal to kill seals in the closed season between 1 September and 31 December under any circumstances. Fishermen may defend their nets from adult seals attacking their nets outside these dates in order to protect their catch, but this must be done in a humane manner.

Tommy Allan, Stewart's solicitor, said his client now accepted that the animals were not close to starvation as he had previously claimed. "Mr Stewart accepts that these animals were healthy and this is something he should not have done. He hasn't put forward any reason why he did do this," Allan said.

East Linga, a tiny and remote island three miles east of Whalsay, is one of the few places in Shetland where grey seals can have their pups. However, the attack was witnessed by Scottish Natural Heritage staff, who were in the area surveying the grey-seal pupping season. About 30 grey seals are born on East Linga each year.

Karen Hall, the SNH area officer who saw the incident from a distance, welcomed the guilty plea. "I am pleased that the court is taking this seriously. It sends a very clear message that this sort of behaviour is not acceptable in our society."

"We were out doing our annual grey-seal pupping survey, and we saw a person on the beach clubbing seals. Following further investigations we were horrified to find 21 pups killed in a brutal manner."