The Basque region is one of Spain's wealthiest, but Juan Jose Ibarretxe, the current Basque regional president and Nationalist Party candidate, launched his campaign on the region's recessionary fears amid the global economic crisis.
Analysts had predicted big gains for the Socialist party, which ran a campaign to retain strong links with the ruling Socialist central government of Jose Luis Rodriguez Zapatero, the prime minister.
According to exit polls, the Socialists gained up to 10 seats, mainly from the conservative Popular Party, but not enough to take control of the 75-seat regional parliament.
The new Basque parliament will be the first to exclude the participation of radical nationalist parties supporting Eta, the armed separatist group.
The Madrid-based Supreme Court in February barred candidate lists submitted by two parties - Askatasuna and Demokrazia 3 Milioi - on the grounds that they were directly linked to the banned Batasuna party, outlawed in 2003 for being Eta's political wing.
Eta has killed more than 825 people during a violent separatist campaign since the late 1960s to try to establish an independent Basque country straddling northern Spain and southwestern France.
The group has called the elections undemocratic and told supporters to post blank ballots.
Any parliament resulting from this weekends polls would be a "fascist parliament", Eta said in a statement published in Gara, a pro-independence newspaper, on Friday.
"For those in favour of independence, of sovereignty, the only vote is blank," it said.
Basque separatist parties are said to have the support of about 10 per cent of the local population, and supporters have complained that the exclusion made Sunday's vote undemocratic.
Karmele Viteri, a 30-year-old teacher, said after casting her vote: "These elections are a farce, they exclude 15 per cent of the Basque electorate."
|Police hold back supporters of Basque separatist group D3M during the vote [AFP]
Around 1.7 million Basques were eligible to vote.
The Basque Nationalist Party, which rejects Eta's violence, insists that Basques have the right to decide by referendum whether to remain part of Spain or break away.
Emilio Ibanez, a 40-year-old industrial engineer, said: "I've voted so that we can have a parliament that'll give us Basques the right to decide if we want to continue as part of Spain or not."
The Socialist party - citing Spain's constitution - maintains that only Spain's central government can invoke referendums.
Regional elections are also taking place Sunday in northwestern Galicia, where the Socialist Party of Galicia and the Galician Nationalist Block could form a ruling coalition again if together they win more seats than the conservative Popular Party.