Thousands protested against the raid in the Basque town of Segura last week, with a senior party official describing it as a "kidnapping" and a "declaration of war" by the government.
"It's obvious the understanding between Batasuna and ETA"
Judge Baltasar Garzon
Four of them were released on $14,000 bail while two others were freed after the court found no direct links to Batasuna.
Eight of the 17 are repeated offenders, a court official said.
"They are not willing to end terrorist violence but to co-help Eta to achieve its aims through violence," Garzon said in his ruling. "It's obvious the understanding between Batasuna and Eta."
Most of those detained refused to answer Garzon's questions, local media reported.
Pernando Barrena, a senior Batasuna member, said Spain had in effect declared war by arresting most of its leadership.
"The repression will not make us back down," he said on Saturday amid protests by thousands in Bilbao, San Sebastian and Vitoria.
Jose Luis Rodriguez Zapatero, the Spanish prime minister, pursued a peace process with Eta after the group declared a ceasefire in March 2006, and saw Batasuna as a potential bridge to Eta separatists.
The ceasefire ended in December following an Eta bombing that killed two people, and led to the arrest of dozens of suspects.
In July, Arnaldo Otegi, Batasuna's most prominent leader, was jailed on terrorism charges.
Eta has been blamed for killing more than 800 people since the late 1960s in a campaign to establish an independent Basque state in northern Spain and southwestern France.
In 2003, Spain's Supreme Court barred Batasuna from running in elections or holding formal meetings for refusing to condemn violence and cut links with the Eta.
Both Batasuna and Eta are listed as terrorist organisations by the European Union and the US.