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.
Present at the media conference were Deputy Youth and Sports Minister M. Saravanan, Olympic Council of Malaysia president Tunku Imran Tuanku Jaafar and Malaysian Sea Games Organising Committee (Masoc) chief executive officer Zolkples Embong.
Malaysia apologised on Sunday for the upside-down printing of Indonesia's flag in the souvenir guidebook for the Southeast Asia Games, which officials said is being withdrawn and reprinted.
"We apologise for affecting the image and reputation of the Republic of Indonesia, as the flag is a symbol of pride", he said after meeting Indonesia's delegation to the games.
Indonesian president Joko Widodo has called for a end to the controversy over a misprint of the Indonesian flag in a 2017 Kuala Lumpur Sea Games booklet.
"Malaysian government has issued an official apology statement just now from the foreign ministry to the Indonesian government", Jamaluddin said.
"Bapak Imam, please accept my honest apologies for this".
Indonesia's flag has a red stripe above a white stripe, but it was printed with the white stripe on top - which made it look like the flag of Poland.
Khairy, who is also Masoc chairman, said he had stopped the distribution of the erroneous souvenir book and a new edition with the appropriate correction would be issued.
Imam Nahrawi had expressed his regrets on the matter via his Twitter account yesterday and Khairy had replied through Twitter to apologise apart from stating the mistake was unintended.
Bukit Aman federal police Special Branch director Mohamad Fuzi Harun said the investigation was to identify the cause. However, we are investigating this matter and will take action as the incident should not have happened.
A Malaysian daily also printed Indonesia's flag upside down, while the Games organisers were criticised for using the wrong flag for two Brunei athletes at a synchronised swimming event.