The Arctic Sunrise "left at 5.00pm local time (1700 GMT) and set off toward Valencia" in eastern Spain, a spokesman for the environmental group said.
Spain said it impounded the ship because the crew defied orders to leave a restricted zone where they were protesting against oil exploration off the Canary Islands.
Spain's maritime authorities have launched administrative proceedings against Greenpeace for a breach of marine traffic rules, Greenpeace International's legal unit told The Local.
On November 15th, three Spanish navy boats rammed vessels in which Greenpeace activists were approaching a ship belonging to Spanish energy firm Repsol, video distributed by Greenpeace showed.
An Italian protester fell in the water and was injured, Greenpeace said. It said its activists were protesting peacefully.
Authorities impounded the boat on November 18 at the port of Arrecife on the island of Lanzarote.
Greenpeace had said the captain, a US national, was being refused release until the €50,000 ($63,000) bond was paid. It had initially refused to pay.
The group expect to see that bond refunded as they believe they will manage to get legal proceedings thrown out of court, they told The Local.
The organization has filed an appeal and is looking at possible legal action against Spain over a "disproportionate" response by the navy, although a final decision has not been made.
The beaches of the Canary Islands, an Atlantic archipelago off northwest Africa, are a popular draw for tourists from Britain, France and elsewhere.
This month's incident was the latest involving the Arctic Sunrise, which was seized by Russian commandos in September 2013 during a protest against Arctic oil drilling.