Dr Tedros Adhanom Ghebreyesus told a press briefing it would have been “inhumane” to leave people on board the ship rather than letting it dock in Tenerife, from where people were repatriated to their home countries.
All 20 British nationals from the MV Hondius, together with a German who is a UK resident, and a Japanese passenger, were flown from Tenerife to Arrowe Park Hospital on the Wirral on Sunday.
Arrowe Park is housing the group for three days in total before they are sent home to continue isolating for a further 42 days.
If people cannot go home, they will be placed in other accommodation to see out the isolation period.
Dr Adhanom Ghebreyesus, director general of the WHO, told a press briefing on Tuesday there was a need for kindness and compassion towards those involved.
He said: “Almost 150 people from 23 countries were on this ship for weeks, in what must have been a very frightening situation.
“Some of the passengers were facing mental breakdown.
“They have the right to be treated with dignity and compassion.
Passengers are sprayed with disinfectant by Spanish government officials after disembarking from the ship (Arturo Rodriguez/AP)
“There were some people around the world calling for the passengers to be contained on the ship for the full quarantine period.
“Our view was that would have been inhumane, and unnecessary. Yesterday during our press conference I called it even cruel to suggest that.
“We were convinced it was possible to disembark these passengers in a way that was safe for them and the people of Tenerife, and that was respectful of the human rights of the passengers and crew.”
The leader praised Spain’s prime minister, Pedro Sanchez, for allowing the ship to dock in the Canaries.
He said that “for the past week, Spain and WHO have worked together closely under Spain’s leadership, along with the government of the Netherlands and the ship’s operator, to coordinate and execute the operation that took place over the past two days.”
He added: “I thank Prime Minister Sanchez not only for meeting Spain’s legal duty under international law, but also for exercising his moral duty to show solidarity with, and compassion and kindness for the passengers on the ship.
“Especially during these difficult times, the world needs this kind of kindness and compassion.
“That’s what exactly Spain did, and we’re so proud to witness that, and I know the whole world is proud to witness that.”
Dr Adhanom Ghebreyesus said WHO could “say confidently” that the process of all passengers leaving the ship to return to their countries “was successful” and he also praised the ship’s captain Jan Dobrogowski and the crew.
So far, 11 hantavirus cases have been reported among people on the cruise, including three deaths.
Nine of the 11 cases are confirmed, with two more probable cases.
“At the moment, there is no sign that we are seeing the start of a larger outbreak,” Dr Adhanom Ghebreyesus told the briefing.
Passengers leave the hantavirus-stricken cruise ship (Manu Fernandez/AP)
“But of course, the situation could change.
“And given the long incubation period of the virus, it’s possible we might see more cases in the coming weeks.”
In a video message on Monday, the ship’s captain Mr Dobrogowski thanked passengers and crew and said “the past few weeks have been extremely challenging to us all”.
He added: “What touched me the most, what moved me the most, was your patience, your discipline, and also (the) kindness that you showed to each other throughout.
“I’ve witnessed your caring, your unity and quiet strength amongst everybody on board, guests and crew alike, and I must commend my crew for their courage and the selfless resolve they showed time and again in the most difficult moments.
“I cannot imagine sailing through these circumstances with a better group of people, guests and crew alike.
The MV Hondius cruise ship departs the port in Praia, Cape Verde (Misper Apawu/AP)
“Most importantly, our thoughts are with the ones that are no longer with us. Whatever I say will not ease this loss.
“I’d like you to know they are with us every day, in our hearts and our thoughts.”
Meanwhile, a French woman who tested positive for hantavirus is in intensive care in stable condition at a Paris hospital.
One of 18 evacuated passengers flown to the US has also tested positive but has no symptoms, while another had mild symptoms.
One British man with hantavirus is still being cared for in Johannesburg and is thought to be improving, while another is in the Netherlands.
Another British national has hantavirus and is isolating where he lives on the remote South Atlantic Island of Tristan da Cunha.