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 on Friday morning, an official from the Korean National Police Agency told AFP.
Livestream footage 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, visited the NEC on Thursday and said the election should be rerun.