"There was an explosion at 12:30am [22:30 GMT on Friday] in the Berriz Euskotren [local train] station. There is very serious material damage and no one was injured," a spokesman for the Basque region's interior ministry.
Police were on the scene "to determine whether it was an act of urban violence or a terrorist attack," he said.
Ticket offices and machines were damaged in the attack in Amorebieta. Molotov cocktails are often thrown at official buildings, stations or automatic teller machines in the region.
The two towns were the blasts took place are situated near the highway linking the Basque cities of Bilbao and San Sebastian.
Eta, listed as a terrorist organisation by the European Union and the United States, is considered to be responsible for 824 deaths during a 40-year-long campaign.
Saturday's blasts came hours after Baltasar Garzon, Spain's most senior anti-terrorism judge, indicted 24 people on charges that they belonged to a ring that extorted money for Eta.
The last attack attributed to the group was on October 4 when a bomb exploded in front of a courtroom in Tolosa. On that occasion a telephone warning was given.