Greenepeace said its Arctic Sunrise icebreaker would leave Russia's Arctic seas after being threatened with gunfire Monday.
Russian authorities reportedly boarded the ship after it entered Russian waters to protest Arctic oil drilling.
Crewmember Christy Ferguson said the crew was told by authorities to leave or risk being fired on.
The Dutch-flagged Greenpeace ship entered the Northern Sea Route Saturday and proceeded to the Kara Sea off Russia's north coast.
The environmental group is protesting offshore oil exploration by Russian state oil giant Rosneft and US company ExxonMobil. Greenpeace says the Russian government has plans to drill in the Russian Arctic National Park, a nature reserve containing whales and polar bears.
The Arctic Sunrise had been asked to leave by the coast guard on Sunday, but refused. Greenpeace activists released banners off their icebreaker reading "Save the Arctic" and deployed inflatable boats.
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Four Russian coast guards then boarded the ship Monday and searched the vessel.
Greenpeace says that Russia is trying to stifle peaceful protest while the Russian government has said that the group defied international law by entering its waters without permission.
When Russia requested that the Netherlands act to prevent a ship flying their flag from entering Russian waters, the Dutch government responded that Greenpeace had an "indisputable" right to peaceful protest.