The mistake prompted fury in Indonesia over the weekend and President Joko Widodo demanded an official apology.
Indonesia's Youth and Sports Minister Imam Nahrawi tweeted several images , saying it was a "fatal negligence that was very painful".
Mr Widodo said Indonesia wanted an official apology "as it concerns the pride and nationalistic spirit of our Indonesian people", according to reports.
Indonesian netizens also complained online, using the hashtag #ShameOnYouMalaysia, and several noted that the upside down flag resembled Poland's.
- Hackers hit Malaysian sites over Indonesia flag gaffeChannel NewsAsia
- SEA Games: Ice hockey makes splash in tropics, puddles and allInquirer.net
- Jakarta protesters say flag wilfully printed upside downFree Malaysia Today
- Upgrade security, advises CyberSecurity following hackingFree Malaysia Today
- SEA Games: PH ice hockey team shuts down IndonesiaABS-CBN News
- Indonesian hackers retaliate flag blunder by defacing M'sian sitesThe Sun Daily
- Malaysia Extends Apology for Indonesia Flag BlunderTempo.co
- Malaysia apologises for showing Indonesia's flag as Poland'sBorneo Bulletin Online
- Indonesian hacker group defaces Malaysian websites following flag blunderThe Star Online