They had hoped for a dream vacation to some of the world’s most remote and breathtaking places. Instead, dozens of cruise passengers remained stuck on a ship Wednesday following a deadly virus outbreak as officials on land clashed over when and where they could get off.

The MV Hondius on Wednesday planned to sail to Spain’s Canary Islands, where its operator, Oceanwide Expeditions, and Spain’s health ministry had said the ship would dock. But Fernando Clavijo, who leads the regional government of the islands, objected to the plan.

“There is no information that justifies why the vessel must sail for three days to the Canary Islands to carry out a task that could be done from Praia,” Mr. Clavijo said in a radio interview, referring to a port in Cape Verde where the ship was denied permission to dock this week.

Since April 11, three passengers who were aboard the Hondius have died and five other people have been sickened after showing symptoms of the hantavirus, a rare family of viruses carried by rodents, according to the World Health Organization. On Wednesday morning, three people aboard the ship — two with “acute” symptoms of the disease — were evacuated on two medical flights to the Netherlands, according to the Dutch foreign ministry.

Two of the evacuees — a 56-year-old British citizen and a 41-year-old Dutch citizen — were workers on the ship, according to Oceanwide, and Spanish officials said that one of them was the ship’s doctor. The third evacuee was a 65-year-old German passenger who had been in close contact with one of the people who died.

“At this stage, the overall public health risk remains low,” Tedros Adhanom Ghebreyesus, director-general of the W.H.O., said on social media.

The MV Hondius departed from Argentina in early April with about 150 passengers and crew members. Antarctica, the Falkland Islands, South Georgia Island, Nightingale Island, Tristan da Cunha, St. Helena and Ascension were among the planned stops on its route.

After the outbreak began, the ship headed to Cape Verde, where officials did not allow passengers to disembark.

Those on board were doing their best to keep busy, some watching movies in their cabins, according to accounts from passengers in interviews and social media posts.

Passengers are encouraged to practice social distancing and wear masks. For meals, they are told to sit in every other chair in the dining room and are encouraged to wash their hands regularly. Hand sanitizer dispensers have been placed around the ship and the staffers are frequently cleaning hand rails and other high-contact surfaces.

“Our days have been close to normal, just waiting for authorities to find a solution, but morale on the ship is high and we’re keeping ourselves busy with reading, watching movies, having hot drinks and that kind of things,” Kasem Hato, a Jordanian travel influencer who posts online as Ibn Hatutta, said in an email.

The first fatality on the ship was a 70-year-old Dutch man who died aboard the ship on April 11. The man’s 69-year-old wife became ill and died on April 26 in Johannesburg, South Africa, while attempting to fly home to the Netherlands. The third fatality was a German passenger who died on May 2.

So far the virus has been confirmed in three of the cases: the 69-year-old woman, another passenger who was taken to a hospital in South Africa and a man in Switzerland, who had disembarked the cruise and was receiving care in a hospital in Zurich.

The National Institute for Communicable Diseases in South Africa said that all three confirmed cases involve the Andes virus, a type of hantavirus which is primarily found in South America and is the only type known to spread between people.

Carlos Barragán, Max Kim and Keith Bradsher contributed reporting.