Basque police, who had kept a low profile during the march,were deployed on to the streets and fired rubber bullets in the air to ward off the attackers. Police chased the attackers into a building in the old quarter, while some onlookers shouted "assassins" at police.
The violence came shortly after tens of thousands of Basques took to the streets in the largest demonstration called by Herri Batasuna, the political wing of ETA, since the killing of a politician by separatist rebels earlier this month.
With Spain still seething over the murder of 29-year-old Miguel Angel Blanco, the Basque authorities had bolstered security surrounding the march. Special vans used by anti-riot police were stationed at strategic points, and a police helicopter hovered over the city.
Herri Batasuna had pledged to keep the protest peaceful and provided scores of private security guards to maintain order. The demonstration itself ended peacefully. Yesterday there was no sign of trouble as more than 20,000 demonstrators chanting "Independence" and "Long live the ETA military" moved peacefully along the beachfront in San Sebastian, a stronghold of the radical Basque separatist movement.
Herri Batasuna, called the march in response to anti-ETA rallies held across Spain in the past two weeks. Addressing cheering supporters, its chief spokesman, Floren Aoiz, accused the government and the media of conspiring to undermine the separatist movement and said that was tantamount to "throwing gasoline on the fire."
He reasserted the group's call for talks between the government and ETA, saying Herri Batasuna "is holding out its hand in the search for peace."