Mikel Sarobe detained along with two members of banned Basque group in Bayonne.
Spanish police are expected to travel to Northern Ireland to question the detained man.
Michelana is said to have had long-term links to Eta, and had first been arrested in 1989.
Eta’s violent campaign to carve out an independent Basque state in northeast Spain and southwest France has resulted in more than 800 deaths since the late 1960s.
The group’s leaders have maintained close links with the outlawed Irish Republican Army (IRA) and its sister Sinn Fein party.
But while Sinn Fein today helps lead Northern Ireland’s government following the IRA disarmament in 2005, an Eta cease-fire in 2006 soon crumbled, leaving its political wing, Batasuna, banned in Spain.