Wednesday's election was the first nationwide vote since President Lee Jae Myung took office following the ouster of Yoon Suk Yeol over his short-lived martial law declaration.

Lee's ruling Democratic Party swept most races but failed to flip the crucial Seoul mayoral seat.

Fourteen polling stations in Seoul ran short of ballot papers, and the National Election Commission (NEC) apologised, blaming a failure to anticipate turnout.

The agency's chairperson, Rho Tae-ak, resigned over the furore on Friday, saying there is "no excuse for the occurrence of an unacceptable incident" that "infringed upon the people's precious right to vote".

He did not, however, mention the possibility of a re-election.

Some polling stations stayed open until 10 pm (1300 GMT) on Wednesday to accommodate voters, but the move did little to quell criticism of the commission's handling of the election.

Protesters holding signs that read "Stop the vote count" and "Invalidate the election" blocked authorities in Seoul's Jamsil 7-dong district from removing two ballot boxes.

A gathering of several dozen people on election night swelled to more than 1,000 protesters by Thursday, Yonhap reported.

Polling station staff were forced to remain inside until Friday morning, according to KBS.

The boxes, containing about 2,000 ballots, were secured and transported to a counting centre after the riot police intervened Friday morning, an official from the Korean National Police Agency told AFP.

Livestream footage of the morning incident showed police physically removing demonstrators blocking entrances to the polling station, with some protesters shouting and resisting.

Heated exchanges followed, with one man shouting, "Is this really a country governed by the rule of law?" as officers repeatedly ordered demonstrators to clear the way.

President Lee on Thursday ordered an investigation into the ballot shortage, condemning "a flaw that is difficult to accept".

People Power Party (PPP) leader Jang Dong-hyeok, whose party suffered a heavy local election defeat after Yoon's martial law declaration, said the election should be rerun.

After declaring martial law, former president Yoon -- now jailed and on trial for insurrection -- claimed the NEC had ignored warnings about North Korean threats to voter data and failed to cooperate fully with intelligence agency inspections.

Yoon's claims resonated with right-wing YouTubers and supporters, who went on to spread unverified election fraud theories online and question the commission's credibility.

South Korean social media was flooded with unverified claims about the police intervention on Friday, including a post alleging a young man who tried to block the transfer of ballot boxes was assaulted by officers and left in a coma, accompanied by a photograph claiming to show him.

The Korean National Police Agency told AFP that claims the man pictured was in a coma were untrue.

The election commission is a constitutional body with limited external oversight, and problems related to "internal discipline, oversight and investigations have long existed in a kind of blind spot", political commentator Park Sang-byung told AFP.

"Worse, it has effectively handed ammunition to election-fraud conspiracy theorists, who will likely exploit the controversy for months," Park said.

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