Izaskun Lesaka, described by Spanish police as among the "three most important figures" in ETA, was arrested Sunday in Macon, ThinkSpain reported.
Another person, identified by the Spanish Interior Ministry as Joseba Iturbide Ochoteco, also was arrested.
Both were said to be armed.
Lesaka controlled ETA's supplies of arms and explosives, the ministry said in a statement.
Twenty-four ETA members have been arrested since January, officials said.
In October 2011, the ETA announced a "definitive end" to its 45-year armed campaign for independence that authorities estimate has cost 800 lives.
Spain has demanded that the ETA disband.