The main opposition group, Al Wefaq, kept its 18 seats in the 40-member legislature. Even without a majority in Saturday's election, it could still forge alliances with liberal parties and others to eventually gain the upper hand in Parliament.
"We really aren't satisfied with the outcome," said Al Wefaq leader Sheikh Ali Salman. As in the last elections, in 2006, the group said there were irregularities, including at least 890 voters being turned away from polling stations because their names were not on electoral lists.
Bahrain's Parliament has only limited powers and can be overruled by the country's King Hamad bin Isa Al Khalifa.
The king opened Bahrain's political system after taking power in 1999 and introduced the parliamentary elections, creating one of the few elected legislative bodies in the region.
In other results, 13 pro-government candidates won seats, and the other nine contests will head to runoffs on Saturday, according to election officials who announced the outcome on state television. Most of the runoffs are between pro-government candidates.
Bahraini officials did not immediately comment on the claims of voting troubles. But Bahrain's justice minister, Sheikh Khaled bin Ali Al Khalifa, said he expected "only a number of infringements" and hailed the voting as fair.