Just minutes before the call was received, police on a routine patrol had spotted a rucksack containing the bomb outside the party's headquarters.
"The agents then cordoned off the area, evacuated a nearby bar and warned local residents with a megaphone," a statement by the police said.
Polls published on Sunday showed the moderate Basque Nationalist Party could lose its nearly 30-year hold on power in the Basque region to the socialists in the upcoming regional elections.
Alfredo Perez Rubalcaba, Spain's interior minister, has said police are on alert for possible attacks in the run-up to the vote.
Eta has been blamed for the deaths of 825 people in a four-decade campaign for an independent Basque homeland straddling northern Spain and part of southwestern France.
The group called off a truce in June 2007, saying it had grown frustrated with the lack of concessions in tentative peace talks on the part of the government of Jose Luis Rodriguez Zapatero, Spain's prime minister.
Eta set off a car bomb at a business park on Madrid's outskirts on February 9, also following a warning call, there were no injuries.
The group also claimed responsibility for the fatal shooting of a Basque businessman and a car bomb outside a Basque television station, both in December.