"We are appalled by Norway's decision to end a peaceful and legal protest," Greenpeace activist Sune Scheller said in a statement.
"We will not stand by while their drilling rigs destroy our last remaining wild places."
Greenpeace said coastguards boarded the ship around 2100 GMT on Friday.
According to media reports, the Esperanza was then towed from the drilling site towards the Norwegian city of Tromsoe, where it is expected to arrive in the next two days.
Earlier on Friday, Norway had created a "safety zone" around the Arctic drilling site to force the departure of the Greenpeace ship.
The zone covered an area of 500 metres (1,640 feet) around the site.
The environmental group is trying to prevent Statoil from operating the northernmost well ever to be drilled in Norway.
"The vessels that are not involved in the oil activities of the operator do not have access to this area," petroleum and energy ministry spokesman Haakon Smith-Isaksen said.
But Greenpeace questioned the legality of the zone arguing that it should have been created with a 30-day notice period.
Before Norway removed the vessel, Greenpeace activist Truls Gulowsen had told AFP that those on the ship intended to stay at least until June 28, the day a 30-day notice period would expire.
"We don't see any reason to move the Esperanza, which has the same right to be on this spot as an oil rig. We even got here first, which according to international law, allows us to stay," he said.
Greenpeace argues that the drilling project in the Hoop area of the Barents Sea is too close to the sea ice and to Bear Island 175 kilometres (110 miles) away, which is home to rare birds and, sometimes, polar bears.
A group of 15 Greenpeace activists boarded the Statoil rig earlier this week and tried to stop the drilling.
The last seven who remained on the ship were removed by Norwegian police on Thursday.
Also on Friday, the Norwegian ministry of climate and environment rejected a Greenpeace appeal asking the government to protect Bear Island and ban drilling in the area.
"We are ready to start the drilling operations as soon as everything will be in place," Statoil spokesman Morten Eek said.