The government of Gibraltar will take action against the captain of a Spanish fishing boat who refused to move his vessel to allow a charity “polar bear swim in disputed territorial waters to go ahead safely.

The Boxing Day tradition of a cold dip in the sea off Gibraltar began with a confrontation between Spanish fishermen and local police at the end of a year that has seen authorities in Madrid and on the Rock at loggerheads over access to the water and other border issues.

As hardy swimmers prepared to take to the sea in Catalan Bay, Royal Gibraltar police officers were alerted to several vessels raking the seabed for shellfish.

When police ordered the Spanish fishing crews to move on for safety reasons, one captain initially refused and a Spanish guardia civil patrol boat arrived at the scene – leading to a one-hour standoff.

The rest of the fishermen, all from the Spanish town of La Línea de la Concepción, moved on when asked to. A government spokesman said had been “more of an accident than an incident but confirmed reports that the captain of Los Mellizos, the boat which did not at first respond to the police order to move, would be reported to a magistrates court.

Gibraltar prohibited fishing with nets and raking the seabed under a 1991 environmental protection law, but has generally allowed exceptions for the neighbouring Spanish fleet. Conflict was stirred in 2013 by Gibraltar’s creation of an artificial concrete reef, something it claimed was designed to boost marine diversity but which was taken by Madrid as a hostile move against Spanish fishermen.

The leader of La Línea de la Concepción’s fishing guild, Juan Morente, put the Boxing Day spat down to a communication problem as the usual prior warning about a special event had not been received in time.

“We were told at 10am that morning and it was too late to stop all the boats heading out, he said.

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