The act was seen as "disrespectful" by fellow MPs.
Japan's Olympics Minister Yoshitaka Sakurada has offered a public apology after he arrived three minutes late to a parliamentary meeting on Thursday.
The minister's "tardiness" was not well received by other members of the parliamentary committee, who considered the act "disrespectful," according to the BBC.
MPs also staged a five-hour long budget boycott in protest of the incident.
Mr Sakurada's apology was his second in a week, after copping criticism for saying he was "disappointed" Japanese swimmer Rikako Ikee announced she had been diagnosed with leukaemia and would not be able to compete at the 2020 Tokyo Olympics.
"She is a potential gold medallist, an athlete in whom we have great expectations. I’m really disappointed," he said.
Mr Sakurada is no stranger to controversy.
He drew criticism in 2018, when he said he'd never even used a computer, despite holding the office of cyber-security minister, adding that his aides always did his computer work for him.
"I've been independent since I was 25 and have always directed my staff and secretaries to do that kind of thing," Sakurada said.
"I've never used a computer."
In 2016, he was heavily criticised for describing Korean comfort women, who were forced to provide sexual services to Japanese World War II troops, as "professional prostitutes".
A recent survey by Japanese Publication Asahi Shimbun found that 65 per cent of people in the country thought he was unsuitable to hold the office of Olympics minister.
Public apologies for being late are not uncommon in Japan. In 2017, a Japanese railway operator issued a deep apology for the 'tremendous nuisance' caused by a train departing 20 seconds early.