Aritz Arginzoniz Zubiarre, believed to be a member of the Basque separatist group, was detained at a bus station in the Spanish port of Santander.
Reports were conflicting about where in Britain the ferry would be headed.
Newspaper El Pais’s website said the suspect had details of at least two potential targets at the time of his arrest. One was the ferry Pont-Aven which links Santander with Portsmouth and another was a court in Santander.
But others reported Spanish police as saying the Pont-Aven, which sails twice a week between Plymouth and Santander and carries up to 2,400 passengers, was one of three possible targets. The Pont-Aven also sails weekly between Cork and Roscoff carrying thousands of passengers between Ireland and France.
Pont-Aven operator Brittany Ferries insisted to media there was no threat to the ferry.
Press coverage, which cited unnamed police investigators, said Arginzoniz Zubiarre was waiting for the arrival of explosives and a car when he was arrested on Tuesday. Newspaper El Mundo said he may have been planning attacks with his girlfriend, named as Saioa Sanchez Iturregi.
He had planned to attack a public building using a car bomb, interior minister Alfredo Perez Rubalcaba told a press conference.
Arginzoniz Zubiarre, the ministry said, had a pistol, a timer and false identity documents when arrested.