"This morning (Tuesday) we registered our protest against this manner of proceeding and the threat of the use of force," said a statement from the Dutch foreign ministry in a translation provided by Greenpeace.
On Monday, the crew of the Dutch-flagged icebreaker Arctic Sunrise chose to leave the vicinity of offshore seismic exploration by Russia's Rosneft and energy multinational ExxonMobil. The decision was made after Russian coast guard officers boarded the vessel without the permission of its captain and warned crew members that they would be fired on if the icebreaker remained.
The confrontation occurred outside Russia's territorial waters, but international law gives Arctic nations some pollution prevention jurisdiction out to 200 nautical miles. Russia had denied the Arctic Sunrise a permit to enter the area over concerns about the ship's ice capability, although Russia has granted permits to dozens of vessels with lesser strength.
Greenpeace argues its vessel was sailing under the right of innocent passage, a long-established principle intended to ensure freedom of navigation on the high seas.
The Dutch government has asked Russia to explain its actions.
"Foreign affairs (Tuesday) summoned the Russian counsellor to the ministry for clarification of the inspection conducted by Russia on the Greenpeace ship Arctic Sunrise. Russia should have sought permission from the Netherlands. So far this has not happened.
"We also asked for an explanation of the reasons advanced to refuse the vessel free passage. That explanation has not yet been provided by the Russian authorities."
The Arctic Sunrise is expected to be clear of the Kara Sea by the end of the week.
At least one Canadian is among the 28 crew members from 15 different countries.