The ministry identified the two men as Jose Javier Oses Carrasco and Ugaitz Errazquin Telleria. Oses is accused of belonging to ETA's urban arm, known as Kale Borroka, and had fled after being let out on parole after a prison sentence.
Errazquin is accused of belonging to an ETA cell that assassinated Socialist politician Isaias Carrasco and businessman Inaki Uria.
The arrests took place in Albi, but the ministry did not say when. Weakened by arrests of most of its leaders and by waning support in Basque Country ETA announced last October the end of its armed struggle, which lasted more than 40 years and claimed more than 800 lives.
But the Spanish government has declined to negotiate a definitive end to the conflict, saying ETA must disband and turn over weapons. A total of 13 suspected ETA members have been arrested so far this year, mostly in France and Spain.