Resignations of shiite opposition MPs were submitted in February over the deadly crackdown on anti-government protesters, but had not yet been approved by the council. The lawmakers acted alongside 11 other Shiite opposition members of parliament whose resignations were previously accepted.
They were members of Al Wefaq, the country's largest Shiite party.
Bahrain's 40-member lower house of parliament is now left with 22 lawmakers and is controlled by Sunnis. Elections to replace the 18 empty seats are scheduled for September.
The lower house was created in 2002 under a new constitution aimed at easing Shiite complaints of perceived second-class status. There is also an upper house of parliament whose 40 members are appointed by the king.
Shiites make up about 70 percent of the population in a kingdom ruled by a 200-year-old Sunni dynasty, but are largely excluded from top government and security posts.
They were the driving force behind protests calling for political reforms that began in February.
Bahraini authorities have been seeking to prosecute opposition leaders and other protesters perceived to be linked to clashes and protests in the Gulf Arab nation.
A special security court set up under martial law sentenced four people to death last month for killing two policemen during the unrest. It is also trying 21 mostly Shiite opposition leaders and political activists accused of plotting against the state.
The country is an important U.S. ally in the region, playing host to the U.S. Navy's 5th Fleet.