Spanish media named the most senior man arrested on Monday as Aitziol Iriondo, and one of the others as Eneko Zarrabeitia.
The arrests follow the December 3 fatal shooting of a 71-year-old businessman in the Basque town of Azpeitia, which the Spanish government blamed on Eta.
Spanish authorities say the group has been reduced to a relatively small number of fighters. But it has continued to carry out regular bombings.
Eta began its violent campaign for the independence of traditional Basque "territories" in northern Spain and southwest France in the late years of the dictatorship of Francisco Franco in the 1960s.
It has killed more than 800 people in four decades.