The blunder came to light at Saturday's opening ceremony in Kuala Lumpur, where the souvenir was handed out to dignitaries - including Indonesia's Sports Minister Imam Nahrawi, who tweeted a picture of the offending page.
The creation of Malaysia when the British Empire was dismantled after the Second World War was bitterly opposed by Indonesia, itself then a new nation emerging from Dutch colonial rule and a short-lived Japanese occupation.
Khairy Jamaluddin met his Indonesian counterpart today to apologise over the flag gaffe in the Sea Games souvenir book following his apology via Twitter last night.
Due to this misprint, the red-and-white Indonesian flag looked like Poland's flag.
President Joko Widodo said here on Sunday that he deeply regretted the incident but called on the people not to make a big problem out of it.
Also present at the media conference were Deputy Youth and Sports Minister Datuk M. Saravanan, Olympic Council of Malaysia president Tan Sri Tunku Imran Tuanku Jaafar and Malaysia SEA Games Organising Committee (MASOC) chief executive officer Datuk Seri Zolkples Embong.
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Ms Ortega, who was sacked after emerging as a top critic of Mr Maduro, said the bribe-taking there went all the way to the top. In the process, Maduro became only the fourth sitting head of state to be sanctioned by the US government.
He said he hoped the incident would not be repeated as the flag was a respected symbol of a country.
"I am expressing my deep regret on this fault, which shows negligence and absent-mindedness", he said in a statement.
But it was not the only incident, as a SEA Games booklet also mixed up Indonesia and Thailand's flags in a reprint of the medals table from 2011. "So police need to take the necessary action and ensure it does not happen again".
Malaysia's Southeast Asian Games organizers have apologized to Indonesia after its flag was printed upside-down in a souvenir magazine, prompting a scathing response from the team and anger on social media.
Susi Susanti doubled the scoreline from the second penalty spot before the break as Indonesia were in control of the match while Malaysia struggled to string passes.
"The matter will not weaken the spirit of Indonesian athletes and it should not be repeated in the future".
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