Malaysia's football body braced for possible punishment on Wednesday after flare-throwing fans forced the abandonment of a World Cup qualifier in ugly scenes which deepened the country's soccer crisis.

The embattled Football Association of Malaysia (FAM), under heavy fire since last week's record 10-0 defeat to UAE, said it was "awaiting the decision of FIFA" after Tuesday's incident.

Militant fans angry at last week's 10-0 humiliation in UAE fired flares billowing orange smoke at Shah Alam Stadium as Malaysia trailed Saudi Arabia 2-1 in the final minutes late on Tuesday.

Players and officials hurried from the field and Saudi fans ran from the stands as flares flew around the stadium. Eleven people were arrested but no one was reported injured.

Asian Football Confederation (AFC) president Shaikh Salman bin Ebrahim Al Khalifa said the regional body was "extremely concerned" and would support any investigation by world authority FIFA.

"The AFC is extremely disappointed with the events which took place on Tuesday and we stress that we take such matters very seriously," he said in a statement.

"This sort of behaviour is deplored by all those who seek to protect the best interests of football in Asia," the Bahraini added.

Malaysia's football body has been strongly criticised by both supporters and the government after a dire run of results culminated in last week's 10-0 loss.

Malaysia's worst-ever defeat followed an earlier 1-1 draw in qualifying at home against lowly East Timor and a 6-0 loss to Palestine.

"FAM views the issue of security as a serious matter, especially the safety of spectators, players and officials in the stadium," an FAM statement said.

Tuesday's conflagration was blamed on the "Ultras Malaya" group of hardcore supporters, who accuse the FAM of incompetence and had threatened to disrupt the match.

FIFA is yet to comment on Tuesday's events.