It was the latest incident involving Greenpeace's campaign boat Arctic Sunrise, which was seized by Russian commandoes in September 2013 during a protest against Arctic oil drilling.
In a protest near the Canaries on Saturday "the Arctic Sunrise violated the exclusion zone and ignored instructions by the (Spanish) navy boat Relampago to abandon the zone," Spain's Defence Minister Pedro Morenes told parliament on Wednesday.
"It launched boats into the sea in order to harass and to try to board the Rowan Renaissance" — the ship that Spanish oil company Repsol is using to explore for oil and gas, he said.
Spain's public works ministry said authorities impounded the boat on Tuesday at the port of Arrecife on the island of Lanzarote and would hold it until a bond was paid.
Greenpeace said the captain, a US national, was being refused release until the €50,000 ($63,000) bond was paid.
On Saturday, three navy boats rammed vessels in which Greenpeace activists were approaching Repsol's ship, video distributed by Greenpeace showed.
An Italian protester fell in the water and was injured, Greenpeace said. It said its activists were protesting peacefully.
The beaches of the Canary Islands, an Atlantic archipelago off northwest Africa, are a popular draw for tourists from Britain, France and elsewhere.
The Dutch-flagged Arctic Sunrise was boarded and seized in September 2013 as it protested at operations by Russian gas giant Gazprom. It was held until June 2014, prompting international protests.