The Dutch-flagged MV Hondius had been carrying around 150 passengers and crew from 23 countries when a cluster of severe respiratory illnesses was first reported to the World Health Organization on May 2.
Three people - a Dutch couple and a German national - have died since the start of the outbreak.
The outbreak on the ship has reached 11 cases, nine of which have been confirmed.
The vessel, operated by Oceanwide Expeditions, had been stranded off Cape Verde, its intended final destination, earlier this month after authorities barred passengers from going ashore due to the outbreak.
The WHO and the EU asked Spain to manage the evacuation at the Canary Islands, after which the ship departed for Rotterdam with a skeleton crew and two additional medical staff.
Local port authorities said quarantine facilities had been set up for some of the non-Dutch crew, though it was unclear if they would stay there for the full recommended 42-day quarantine period. The vessel itself was to undergo disinfection.
Hantavirus is primarily spread by rodents but can be transmitted between people in rare cases and after prolonged, close contact. Incubation can last about six weeks.
Crew, passengers who already left the ship and people in contact with them have been quarantined in several countries around the world.
The current outbreak involves the so-called Andes virus, which has circulated in Argentina and Chile for decades.
Ship samples show no meaningful variation in the virus, the European Centre for Disease Prevention and Control has said.
The WHO recommends monitoring and quarantining high-risk contacts for 42 days after exposure, while advising low-risk contacts to self-monitor and seek medical care if symptoms develop.
Public health officials will inspect the vessel before it is allowed to sail again. The hantavirus outbreak aboard the MV Hondius is the first known case on a cruise ship.
The Dutch company that owns the cruise ship said it doesn't foresee any changes to its operations. It has an Arctic cruise setting sail from Keflavik, Iceland, on May 29.
France's Pasteur Institute said on Saturday it has fully sequenced the Andes virus detected in a French passenger from the MV Hondius cruise ship and found it matched viruses already known in South America, with no evidence so far of new characteristics that would make it more transmissible or more dangerous.
