Almost the entire suspected leadership of Batasuna was detained in a police raid in the town of Segura on Thursday night while its executive committee was holding a secret meeting, police and court officials said.
Barrena said on Friday that the raid was revenge for the movement's hard-line position in stalled peace talks and was carried by the Socialist party to improve its position before elections next March.
The arrested Batasuna members are due to be questioned on Sunday by Baltasar Garzon, the anti-terrorism judge who ordered the arrests.
A judicial source said after the arrests that the suspects face charges related to Garzon's investigation into links between Batasuna and Eta, especially the political party's suspected financing of Eta's activities.
Spanish radio said that the suspects were being transferred to Madrid on Saturday, but police searches were continuing in the Basque region.
|Barrena is the most senior Batasuna official |
still at liberty [File: EPA]
Premises reportedly raided included a property belonging to the Communist Party of the Basque Lands, which is allied to Batasuna but not banned.
Late on Saturday, several thousand people gathered in Bilbao, San Sebastian and Vitoria protest against the arrests.
The banner leading the march at Bilbao declared, "Open the doors to independence and long live the free Basque Country."
In San Sebastian, one written in the Basque language, read: "You will pay for what you have done."
The demonstrations followed similar displays on Friday night.
Meanwhile, there were sporadic incidents of violence across the Basque Country, including the burning of a post office on Saturday, regional police said.
There was also an attempt to set a bus on fire at Markina and petrol bombs were thrown at a courthouse and municipal office building in Pasai San Pedro.
Both Batasuna and Eta are listed as terrorist organisations by the European Union and the US government.
Batasuna was outlawed by Spain's supreme court in March 2003 refused to condemn violence and cut its links to Eta.
Eta has been blamed for more than 800 killings since the 1960s in a campaign to establish an independent Basque state from parts of northeastern Spain and southwestern France.
The group called off a ceasefire in June after peace talks with the Spanish government broke down. Its last major attack took place in December 2006, when a bomb at Madrid airport killed two people.