Mr Widodo said the incident "concerns the national pride of our country", but added: "We deeply regret the incident but do not exaggerate it".
Indonesian netizens, still smarting from their upside-down flag printed in the official progamme book, were inflamed again when a newspaper's SEA Games graphic centrespread was found to contain the same mistake.
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 error made the red-and-white Indonesian flag resemble Poland's and caused anger in Indonesia, where "shameonyoumalaysia" has become the most popular hashtag on Twitter.
Indonesia had been quick to point out the mistake, with their Olympic committee chief, Inter Milan president Erick Thohir, slamming Malaysia's "negligence".
"Friendship is the greatest legacy in sports, but a mistake in presenting a national identity is not justified", he said.
Malaysian police are investigating the matter. We are investigating and will take action as the incident should not have happened.
The Indonesian flag was printed upside down in the souvenir booklet, prompting fury and a demand for an official apology. He has asked his fellow Indonesians to put aside the problem and move on with the games.
Brunei has also had its flag misused after organisers used the flag of the Brunei military rather than the country when awarding synchronised swimmers Jacqueline Lim and Nur Hafizah Ahmad their medals, according to a report from Agence France Presse.
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