The largest opposition party, Wefaq, walked out of 18 seats after security forces killed protesters at the start of pro-democracy demonstrations in February that echoed the Arab Spring movement sweeping other countries in the region.
In 14 districts, only 25,130 voters of a total 144,513 came out to vote, a 17.4 percent turnout, according to figures published on the government's elections website www.vote.bh. All the candidates are independents who would have found victory a tall order without the boycott.
Voting did not take place in four districts where candidates were running uncontested and automatically won the seat. Of the 14 contested seats, another poll will be held for 9 seats on Oct. 1 since no candidate was able to win a majority.
The low turnout was a victory for Wefaq which called on voters to boycott the by-elections. Wefaq had predicted a 15 percent turnout and the government had said it was hoping for at least 30 percent. In the United Arab Emirates, a nearby Gulf country that also held elections for an advisory council on Saturday, voter turnout was below expectations at 28 percent.
After calling in Saudi troops and imposing martial law to quell the February protests, the government began a national dialogue that has proposed reforms that opposition groups say fall short of their demands for a transition to democracy.
The proposals allow for increased parliamentary monitoring of government ministers, but do not give the elected body real legislative powers.
King Hamad bin Isa al-Khalifa appoints an upper house and his uncle, Sheikh Khalifa bin Salman, has been prime minister for four decades. Bahrain, an island state that hosts the U.S. Fifth Fleet, remains deeply divided.
The Sunni Muslim monarchy says the protest movement and opposition groups had a Shi'ite sectarian agenda and were acting in coordination with non-Arab Shi'ite power Iran. The opposition denies this and says the claim is an excuse for the ruling elite to avoid giving up their monopoly on power.
The justice minister said the turnout had been a victory for Bahrainis against "sectarian division". "There is a popular will to create the present and the future and challenge the sectarian division that some want to create," Sheikh Khalid bin Ali al-Khalifa told reporters on Saturday. He said some people had been arrested for trying to disrupt voting.
"We are not in a political crisis, but we have a problem in Bahrain and the main issue is how to move forward." The government blamed the low turnout in some districts on voter intimidation.
"What is clear is that in areas where Bahrainis were allowed to freely exercise their democratic right, turnout was high... what is also clear is that in areas where voters had rocks thrown at them, road blocks put in their way and where they suffered sickening intimidation, turnout was low," Bahrain's Information Affairs Authority said in a statement.
But Wefaq leader Sheikh Ali Salman, a Shi'ite cleric, said the results showed Bahrainis rejected the king's reforms and the government faced a stark choice between a move to democracy or "dictatorship".
"There is no such thing as 'Bahraini democracy', there has to be peaceful rotation of power," he told a news conference at Wefaq headquarters in Manama. "If there is no transition, Bahrain will remain in a crisis of security and human rights. This is a historic moment."
Though martial law ended in May, clashes continue almost nightly in many Shi'ite areas of the country, whose profile as a banking hub has been dented by the turmoil.
Michael Stephens, a researcher at the Royal United Services Institute (RUSI) in Qatar, said the election amounted to a referendum on the king's national dialogue and the country now faced a dangerous stalemate.
"Given what King Hamad has said about the urgent nature of reforms, the question is if he can deliver. If he doesn't then I think Bahrain's in serious trouble," he said. "You'll see an escalation of violence."