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.
It was conveyed by Khairy at a meeting with his Indonesian counterpart Imam Nahrawi here today.
The post Malaysia Apologises To Indonesia Over Flag Blunder appeared first on Channels Television.
"We would like to sincerely apologize to the people of Indonesia for the inadvertent error of publishing the wrong flag for Indonesia", SEA Games organizers said in a statement.
Malaysia's foreign ministry and the Games organisers apologised profusely for the gaffe but it was not enough to quell a wave of complaints online, with #ShameOnYouMalaysia becoming Indonesia's top trending topic on Twitter.
The two met behind closed doors for 10 minutes, and later told a press conference that the issue was now resolved.
On Saturday, immediately after being alerted to the mistake, Khairy tweeted his apology.
"The official apology will include my official apology to Bapak Imam verbally as well as in written form to express Malaysia's regrets as hosts over the incident". There was no malice.
"We deeply regret the incident but do not exaggerate it", he said.
Mr Khairy said the mistake was "unintentional and it happened due to our carelessness".
"We don't want our neighbouring country, Indonesia, to feel hurt, so we need to take measures to ensure this does not recur in future".
Bukit Aman federal police Special Branch director Mohamad Fuzi Harun said the investigation was to identify the cause.
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.
He said this after witnessed the outgoing Johor police Chief Comm Datuk Ahmad Najmuddin Mohd handing over duties to the new Johor police chief DCP Datuk Mohd Khalil Kader Mohd at Johor police contingent headquarters today.