The vote comes nearly two months after the emir, Sheikh Sabah al-Ahmad al-Sabah, dissolved a pro-government parliament following its reinstatement in June by a court ruling that also annulled an assembly elected in February.
Prominent opposition figure and former MP Faisal al-Muslim claimed on his Twitter account that three hours before the polls were due to close, turnout was around 17 percent.
A number of opposition figures also charged that some voters had been given two ballot papers in a bid to create the appearance of a higher turnout.
"The Kuwaiti people have succeeded in bringing down (this) election by not taking part," opposition leader and former MP Mussallam al-Barrak said on Twitter.
Former parliament speaker and opposition leader Ahmad al-Saadun said Friday's opposition march and the boycott had taken away "popular and political legitimacy" from the next parliament and government.
Waleed al-Tabtabai, a former Islamist MP, said on Twitter that turnout would not exceed 15 percent. In February, about 65 percent of those eligible voted.
The Popular Committee for Boycotting Election warned the government against any attempt to manipulate the results and turnout, saying that it has closely monitored polling.
Information Minister Sheikh Mohammad Abdullah Al-Sabah played down the figures released by the opposition, telling state television the independent National Election Commission was the only authority to issue such information.
The minister also said an international observer team is in Kuwait to monitor the election along with local people.
Former Shiite MP and candidate Ahmad Lari accused the opposition of publishing "lies" in a bid to cover the fact that turnout was high.
Predominantly tribal constituencies led the way with the boycott, as voters appeared to heed the appeal by both their chiefs and the opposition to stay away from polling over a disputed electoral law.
More activity was seen in other districts, but the highest turnout was in districts populated by the Shiite minority, according to an AFP correspondent and witnesses.
State media and senior officials continued to urge citizens to cast their vote in order to achieve political stability in the oil-rich Gulf state.
In the area of Salwa, 15 kilometres (10 miles) south of the capital, only a few people showed up after the centre opened.
In the nearby area of Rumeithiya, there was more activity in the predominantly Shiite constituency but still far below that in February poll or in 2009.
"I believe that voting is a national duty especially after the emir has urged us," Nadya Mandani, a public sector employee told AFP after voting in Rumeithiya.
"I am very optimistic that the next parliament will be good and will cooperate with the government to resolve our problems," she said.
On the eve of the election, the fifth since mid-2006, tens of thousands of opposition supporters staged a massive demonstration to urge voters to boycott the ballot over the electoral law.
The opposition, which held 36 of the 50 seats in the scrapped parliament, has not fielded candidates among the 306 hopefuls, which include 13 women.
Under previous elections, voters were able to pick up to a maximum of four candidates and this was reduced by the amendment to just one. Each of Kuwait's five constituencies elects 10 lawmakers.
Analysts see little hope the election will bring political stability to the wealthy Gulf state, which has been rocked by lingering disputes stalling development despite abundant petrodollars.
OPEC member Kuwait has a population of 3.8 million, but 69 percent are foreigners. Only 422,000 people are eligible to vote among Kuwaitis, who number 1.2 million.
Polling closes at 8:00 pm (1700 GMT) after 12 hours of voting.
Ahmad al-Ajeel, head of the National Election Commission, established for the first time, said the results would be announced before midnight.