He named one of the detained as Alberto Machain Beraza, who has been on a wanted list since a bomb attack last month on the Spanish island of Mallorca in which two police officers died.
The other two were named as Andoni Sarasola and Aitzol Etxaburu. The Spanish authorities believe Etxaburu has ties with Mikel de Garikoitz Aspiazu, a suspected Eta chief arrested in November in France.
Rubalcaba said there was "no evidence" linking any of the three to the Mallorca bombing or another attack in the northern town of Burgos at the end of July which hurt more than 60 people.
Jose Luis Rodriguez Zapatero, Spain's prime minister, said the arrests were ""a new demonstration of the strength and effectiveness of the fight against terrorism".
"We will continue to eradicate this unacceptable and intolerable stain of violence and terror," he said.
Eta, which was formed 50 years ago, is blamed for the deaths of 828 people in its campaign for an independent Basque homeland in part of northern Spain and southwest France.