The MV Hondius is to sail on from Cape Verde to the Canary Islands despite opposition from the regional government after the death of three passengers.
Two crew members and a British doctor who are all infected or had been in contact with one of the dead flew out on the air ambulances, the World Health Organisation and Spain's health minister said.
AFP footage showed a small red ambulance boat crewed by staff in hazmat suits and masks arriving next to the ship and accepting three people from the boat, who stepped gingerly on to the smaller vessel from a side door. Other passengers gathered on the front deck to watch.
AFP confirmed that two planes later took off from the airport in Cape Verde's capital, Praia, one of them bound for Amsterdam.
Spain's Health Minister Mónica García Gómez said the MV Hondius would dock at Granadilla on the Canary Island of Tenerife by Saturday and passengers, except the most seriously ill, would then be repatriated.
The head of the islands' regional government, Fernando Clavijo, said he opposed any passengers landing there because of the "total absence" of information from the central government over the risks.
In statements to Onda Cero, Clavijo criticized the Spanish government for its "institutional disloyalty" and lack of professionalism for not keeping him informed.
"I cannot allow it to enter the Canary Islands," he insisted, adding that he had demanded a meeting with Spanish Prime Minister Pedro Sánchez.
The vessel has been at the centre of an international health scare since Saturday, when the UN's health agency was informed that three passengers had died and the suspected cause was hantavirus. The rare disease is usually spread from infected rodents, typically through urine, droppings and saliva.
The WHO has said there are two confirmed cases of hantavirus and five suspected from the ship. Three of the people -- a Dutch couple and a German -- have died.
With additional reporting by Alex Dunham, The Local Spain's Editor
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