Oscar Zelarain and Andoni Otegi are accused of putting a bomb inside a stolen Ford Escort and parking it next to the living quarters of the Guardia Civil station in the seaside town.
The suspects allegedly armed the bomb to explode at dinnertime, when most police officers and their families would be sitting down to dinner, ThinkSpain reported Monday.
While the Basque separatist group ETA usually makes an anonymous warning call before a bombing, neither Zelarain nor Otegi gave any warning, prosecutors said.
Silvia Martinez, 6, daughter of a Guardia Civil officer, and Cecilio Gallego, 57, who was waiting for a bus, were killed in the blast.
Fifty-five other people were injured.