It is learnt that the pullout, which was confirmed by the Asian Football Confederation, may affect all the teams in the qualifiers, including Malaysia, as the results against last-placed teams in all groups will not be counted
In Group G, Indonesia are currently bottom, and Malaysia have won both their matches against them in Jakarta (3-2) and in Kuala Lumpur (2-0).
National coach Tan Cheng Hoe said the morale of the players would be affected if the results against Indonesia were not counted.
"But I have told the boys to focus on their games ahead and not about the withdrawal. We will wait for AFC’s further decision, but players know that the next three games will be crucial," said Cheng Hoe.
In their Group G qualifiers in Dubai, Malaysia face United Arab Emirates at Zabeel Stadium on June 3, Vietnam (June 11) and Thailand (June 15).
Malaysia are second in the group with 9 points, while Vietnam lead the standings with 11 points.
Meanwhile, twenty players reported for training yesterday except for Syahmi Safari, who will join them today. Overseas-based players like Dominic Tan, Junior Eldstal, Luqman Hakim Shamsuddin and Liridon Krasniqi will head straight to Dubai on May 20.
"So far, all the players reported without injuries," said Cheng Hoe.
"We have 18 days to prepare before the qualifiers, which is good and we have two friendlies arranged.
Cheng Hoe admitted that the absence of defender Shahrul Saad, who is nursing a knee injury, was a big blow but believed he still has the depth.
"It's a big loss as he has been with me since I took over the team in 2017. We have other players who can help like Dominic, Junior, Adam (Nor Azlin) and Irfan (Zakaria)."