The Legislative Council election - in which only candidates deemed by the government to be "patriots" can run - has been criticised by some activists, foreign governments and rights groups.
Hong Kong government leaders have been urging people to vote, saying the poll is representative. They insist the overhaul, like the security law imposed last year, was needed to ensure stability after protracted protests that rocked the Asian financial hub in 2019.
Turnout has been at the core of election debates, with the government on Saturday sending blanket text messages to Hong Kong residents urging people to vote and some critics calling on people to stay away as a protest.
It is a crime in Hong Kong to incite someone not to vote or to cast an invalid vote.
Turnout was running lower than the last legislative election in 2016, according to government figures.
After five hours of voting on Sunday, official figures showed 14.3 per cent of the electorate had voted, down from 18.88 per cent at the same point four years ago. The previous election turnout was 58 per cent, while the 43.6 per cent in 2000 was the lowest since Britain returned the city to Chinese rule in 1997.
Chief Secretary John Lee, a former security chief, urged people to turn out, saying those excluded were "traitors" who wanted the vote to fail.
By mid-afternoon, volunteer supporters were still pressing flyers on passersby near quiet polling booths, lampposts festooned with flags.
In working class Wong Tai Sin district, a loudspeaker ran on a loop with a recorded plea from Starry Lee, the head of the largest pro-Beijing party DAB: "The situation is critical ... I urge everyone to vote."
Lee's appeal did not convince Wong Tai Sin fruit seller Jack Ng, who said would not join an election that was neither fair nor democratic. "I don't understand why she (Lee) is campaigning. She will win for sure, it is absurd," said Ng, who is in his 20s.
Polls close at 10:30pm (0130 AEDT), with results not expected until Monday.
Hong Kong leader Carrie Lam, among the first to vote, told reporters at a polling station in the suburban Mid-Levels district that the government "had not set any target" on the turnout rate, and she was not aware of any set by the Chinese leadership.
Before Lam spoke, several protesters from the League of Social Democrats opposition group chanted demands nearby for full universal suffrage and waved a banner reading "forced to be silent ... spirit of freedom, vote with your conscience".
Security was tight around the city, with 10,000 police and some 40,000 government election workers deployed.
In the run-up to the election, more than 10 people were arrested for allegedly inciting people to cast blank ballots, including people who had reposted social media posts from others, according to government statements.
China's parliament in March announced sweeping changes to Hong Kong's electoral system, including reducing the number of directly elected seats and setting up a vetting committee to screen all potential candidates, saying only "patriots" may administer the city. More than a third of the seats will now be selected by a committee stacked with Beijing loyalists.
An ongoing crackdown on Hong Kong under the China-imposed national security law has also jailed scores of democrats , while civil society groups have disbanded.
