Four other people were arrested in raids in and near Bayonne in southwest France. One is a suspect in ETA's last killing - the shooting of French policeman in a botched car robbery outside Paris in March, Interior Minister Alfredo Perez Rubalcaba told reporters.
He identified the alleged ETA leader as Mikel Kabikoitz Carrera Sarobe, said he was the instigator of major ETA bombings last summer in Spain, one of which killed two policemen on the Mediterranean island of Mallorca.
"He is the maximum leader of ETA right now. He was responsible for its military branch, and thus directed the commando units," Perez Rubalcaba said. Carrera Sarobe was ETA's most wanted suspect for Spanish police.
Another detainee, Arkaitz Agirregabiria, has been identified by witnesses as a suspect in the shooting outside Paris and was the French police's most wanted suspect, the minister said.
Agirregabiria was the ETA leader's number two man and would have replaced him had Agirregabiria not been arrested himself, he added.
The ministry and French police said the detainees were arrested in Bayonne or nearby Urrugne. The raid was staged by French police and Spanish Civil Guards.
One of the detainees is the girlfriend of a Frenchman who had been under surveillance and whose movements led to Thursday's arrests.
ETA is seeking an independent Basque homeland in northern Spain and southwestern France. It is considered a terrorist organization by the European Union and the United States.
It has killed more than 825 people since the late 1960s.
