"I am truly disappointed by the fans' behaviour," said Ong Kim Swee, who came in as stand-in coach after the UAE debacle cost former handler Dollah Salleh his job.
"While the fans' support is important for any team, what they did last night has damaged the image of Malaysia. Already the image of Malaysian football is suffering."
Malaysian football has been damaged by a rising hooliganism problem along with a steady flow of match-fixing scandals in the domestic leagues.
Police fired tear gas to disperse rioting fans, arresting 25 people, after a Malaysia FA Cup semi-final in May, and last December, five Malaysia supporters were arrested for attacking Vietnamese fans during a heated Suzuki Cup semi-final.
On Wednesday, officials wondered how flares and fireworks were allowed into the stadium despite a heavy security cordon involving hundreds of personnel.
"I am dumbfounded, as despite the tight security outside and inside the stadium fans still smuggled banned items," FAM deputy president Mokhtar Ahmad was quoted saying by the New Straits Times.
"There were only 10,000 fans in the stadium but yet the security could not control them," he added, calling on police to explain.
But Malaysian sports minister Khairy Jamaluddin, who even talked of suspending the FAM after the 10-0 loss, again pointed the finger at the football body tweeted about the incident.
FAM president Tengku Abdullah Ahmad Shah had said on Monday he would "step down in stages" over the 10-0 drubbing.
FIFA is yet to comment on Tuesday's events.