"Here, from the scene of destruction just a few days after this terrible attack, I want to say that my energy and determination to see the end of violence, to reach peace, is even greater," Zapatero said, as rescue workers searched for a likely second victim in the rubble of a multi-storey car park.
Hours later, police said they found 100kg of home-made explosives in a container in the Basque Country town of Atxondo.
They said they suspected it was left there by Eta.
Zapatero's hesitant initial reaction to the blast, in which he was unclear about whether talks were finished or not, and his five-day delay in visiting the bomb site have provided easy targets for the conservative opposition.
Mariano Rajoy, the leader of the opposition Popular Party (PP), who had opted for the high-risk strategy of opposing peace talks, was photographed at the bomb scene two days ago.
More talks with the Basque separatist group, which has killed more than 800 people in 40 years of armed struggle for independence, would now seem unlikely before general elections early next year.