The raid on Thursday led to the arrest of eight members of the group, including a lawyer thought to be the main link between imprisoned Eta members and the group's leadership.
Eta is blamed for the deaths of 829 people in a four-decade campaign of shootings and bombings for an independent Basque homeland in northern Spain and southwestern France.
"The tentacle that allowed Eta to control prisoners has been broken up," Interior Minister Jorge Fernández Diaz told reporters.
But it later emerged the raid had nearly been jeopardized by the press chief of Spain's Interior Ministry.
Albert Gimeno tweeted about the sting operation before it had actually happened.
That information was retracted minutes later but the interior ministry on Thursday announced that the public prosecutor on with Spain's National Court would decide whether an investigation was warranted.
But on Thursday afternoon Gimeno presented his resignation, Spanish news agency Efe reported.
That resignation was accepted on Friday with Interior Minister Jorge Fernández Díaz thanking Gimeno for his service.
Also on Thursday, Spain's Prime Minister Mariano Rajoy told members of the ruling Popular Party he hoped to introduce a law which would prevent ex-members of Eta from becoming mayors, El País newspaper reported.
Spain's current laws do not prohibit ex-members of terror organizations from holding office.
Eta has been weakened in recent years by the arrests of its senior leaders in Spain and France, whose security forces cooperate closely in fighting the band.
The armed group announced in October 2011 "the definitive end to its armed activity", but refused to formally disband and disarm as the Spanish and French governments demand.
Groups supporting the prisoners say there are about 520 prisoners who remain affiliated to Eta, most of them in jails in Spain and France.
Dozens of Eta convicts have been released under a ruling in October by the European Court of Human Rights, which overturned a Spanish judicial doctrine that had extended the time prisoners faced behind bars.