Indonesia has accused the Malaysian organisers of the Southeast Asian Games of negligence after the Indonesian flag was printed upside down in a souvenir guidebook.

The mistake, which makes the red-and-white Indonesian flag resemble Poland's, has caused anger in Indonesia where "#shameonyoumalaysia" has become a popular hashtag on Twitter.

Indonesia's Olympic Committee chairman Erick Thohir said the mistake "shows negligence" and demanded the guidebook be withdrawn and a new version printed.

"Friendship is the greatest legacy in sports, but a mistake in presenting a national identity is not justified," he said.

Indonesia appears to have taken particular offence because the guidebook was distributed to VIPs at Saturday's opening ceremony in Kuala Lumpur for the 29th Southeast Asian Games and only its flag was shown incorrectly.

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Youth and Sports Minister Imam Nahrawi said the error was "very painful".

Malaysia apologised to Indonesia on Sunday for the "unintentional" mistake. Youth and Sports Minister Khairy Jamaluddin met Nahrawi to personally apologise. After a brief private meeting, the two ministers shook hands at a news conference.

Khairy says the guidebooks will be corrected and reprinted.

"We very much regret the mistake," said a Malaysian statement.

Malaysia and Indonesia are both Muslim majority nations and share a similar language but often trade accusations of stealing the other's food and culture.

The creation of Malaysia when the British empire was dismantled after World War II was bitterly opposed by Indonesia, itself then a new nation emerging from Dutch colonial rule and a short-lived Japanese occupation.

On Twitter, Indonesians said their flag represents the sacrifices of independence heroes and accused Malaysia of either being stupid or deliberately misprinting it.