Police seized Ivon Fernandez Iradi on Thursday in the town of Mont-de-Marsan.
Iradi and a second, as yet unnamed, ETA member did not resist arrest - although both men were armed.
Police seized weapons, documents and a computer from their apartment, where they also arrested a woman also believed to be a possible separatist.
Iradi had been sought by police since he escaped from custody in the southwestern city of Bayonne in December last year by squeezing out through his cell's skylight window.
But security services said they only identified the three persons held after they were arrested.
They are being remanded in custody in Mont-de-Marsan, amid tight security.
Spanish Interior Minister Angel Acebes immediately congratulated French police on the "large-scale operation" that led to the arrests.
He described the suspect as "one of the top figures in the ETA terrorist organisation who was largely in charge of commando operations, that is to say the head of the assassins, commandos who commit attacks, those who stage car bombing."
Acebes added that since his escape, Iradi had been reincorporated into the ETA leadership with responsibilities similar to those he held earlier.
Also known under the alias Susper, he is accused of being a member of the so-called "Buruntza" or "Donosti" cell and of seriously wounding a French police officer in November 2001.
Police authorities have also blamed the Donosti commando group for an abortive attack in January 2001 against Spain's ruling Popular Party.
30 year campaign
ETA's armed campaign for a separate homeland in northern Spain and southwestern France has left an estimated 800 people dead over the past three decades.
At the time of Fernandez Iradi's initial arrest - three days before his escape - he was to have been transferred to Paris with seven other alleged ETA members.
His escape led Interior Minister Nicolas Sarkozy to order the suspension of five officers from the Bayonne police station.