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BAFA was suspended by world football governing body FIFA in September 2009 because of government interference in the affairs of the AFC Member Association.
Brunei’s disqualification will see only three teams battle it out in Group A of the qualification - Australia, Indonesia and Myanmar.
Group B comprises Malaysia, Vietnam, Cambodia and the Philippines.
The qualifiers kick off on February 20 and all the matches will be played at the Tennis Indoor Stadium in the Indonesian capital of Jakarta.
The top three teams from the ASEAN zone go through to the Finals, which will be held in Tashkent, Uzbekistan, in May this year.