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THE freighter Horncliff, which ran into difficulties more than 220 miles south west of the Isles of Scilly with 31 people on board, was heading for Dover at the time.
The captain was airlifted to hospital on Saturday with spinal injuries and suspected internal bleeding.
He was one of three people injured on board the Horncliff which it encountered rough weather and lost 60 containers overboard.
Built in 1992, the 12,887-ton refrigerated ship is a frequent visitor to Dover cargo terminal, discharging thousands of tonnes of bananas and pineapples from Costa Rica.
The alarm was raised at 12.30pm on Friday when Falmouth Coastguard received a message that the captain was seriously injured and two passengers also required medical attention. All the deck cargo had been lost overboard.
An attempt to airlift the captain to hospital on Friday night had to be aborted because of the rough weather, but he was successfully rescued by helicopter on Saturday morning and taken to hospital in Truro.
Five others were also taken off the ship which then headed for Falmouth.