The affected websites display a message in red and white - Indonesia's flag colours - which says: "My national flag is not a toy!"
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.
Imam's tweet received a prompt response from his Malaysian counterpart, Khairy Jamaluddin, who apologized through the social media platform and said "absolutely no malice was intended".
Southeast Asia Games host Malaysia has found itself in hot water after an apparent design flaw in the Games' official booklet drew criticism from Indonesian netizens and government officials.
Mr Widodo said Indonesia wanted an official apology "as it concerns the pride and nationalistic spirit of our Indonesian people", according to reports. After a brief private meeting on Sunday, the two ministers shook hands at a news conference.
Khairy, who is also MASOC chairman, said he had stopped the distribution of the erroneous special souvenir book and a new edition with the appropriate correction would be issued. He has asked his fellow Indonesians to put aside the problem and move on with the games.
Khairy Jamaluddin said that the flag printing mishap was unintentional and purely a technical mistake.
"The incident is real and we are doing the investigation, monitoring and working closely with other agencies to mitigate this incident", he said in a statement. The Sepaktakraw Association of Indonesia (PSI) today admitted that walking out of the match against Malaysia was a big mistake and apologised for the action and inconvenience caused.
At the 2012 Olympics, North Korea's women's footballers refused to play, delaying the start of their game with Colombia, when they were shown next to the South Korean flag on a stadium screen.
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