Inaki Reta de Frutos, 56, and Xabier Goyenexea Irragori, 35, were on Spain's most-wanted list and believed to be in charge of logistics for the armed group, which began a unilateral disarmament programme last year.
They have been charged with conspiracy to commit a crime, owning and transporting weapons and carrying false documents, all linked to a terrorist group, a police source said Sunday.
Three other people - a couple and the owner of the house in Osses in the French Basque country where the two men were arrested - were charged but released under judge's supervision.
Goyenexea Irragori is likely to be one of six alleged Eta members to stand trial in the autumn over the death of French police officer Jean-Serge Nerin in a shoot-out that broke out during a routine identity check near Paris five years ago.
The other man accused of opening fire is the former head of the organisation's military wing, Mikel Carrera Sarobe.
Although Eta announced that it had stopped armed actions in 2011, it is still on the European Union's list of terrorist organisations and is held responsible for the deaths of 829 people during its armed campaign for Basque independence.
Its members used to take refuge from Spanish police in the French Basque country but the two countries have increased cross-border cooperation and cracked down on the group.