The mauling in Manama raised suspicion because Bahrain needed a huge turnaround to have any chance of reaching the fourth round of regional 2014 qualifiers.
Bahrain had to beat Indonesia, hope Qatar lost to Iran and also make up a nine-goal difference on the 2022 World Cup hosts.
FIFA’s security department has launched a routine probe, which the AFC said on Friday it supported and would “cooperate closely with”.
Soosay later issued a second statement expressing his belief that the suspicions of foul play were groundless.
“I have read the media reports about suspicions of match-fixing,” he said. “But I am confident that none of our teams are involved in this. Bahrain were the better team both tactically and technically.
“Moreover I have gone through the official reports of the AFC match commissioner and the match referee and they indicate nothing.”
Prince Ali Bin Al Hussein of Jordan – Asia vice president on the FIFA Executive Committee – was keen to stress that while match-fixing should not be taken lightly, it was not just an issue for his region.
“It has to be taken very seriously regardless of what region it is played in. It is a world issue, not just simply in the Asian region,” he told Reuters in London.
“We need to put as much resources as we can into this aspect of football and support those who are dealing with it in FIFA.
“The important thing is that if there are suspicions you have to investigate it.
“It might just be a coincidence, however there might be something behind it. Regardless, it can happen in any country in the world.”
Bahrain’s 10-goal rout almost sent them through but Qatar advanced after an 86th-minute goal gave them a 2-2 draw and the point they needed in Tehran to clinch second place in Group E.
Indonesia, already eliminated, fielded a inexperienced side of mostly uncapped under-23 players after they were blocked by the country’s federation from selecting their regular squad because they mostly play in the breakaway Indonesian Super League.
The size of defeat marked a new low for Indonesian soccer, already torn apart by internal strife and political wrangling.
Indonesia finished bottom of Group E with no points, conceding 26 goals and scoring just three, the worst record of the 20 teams in the third round of Asian qualifying.
“We apologise to the people of Indonesia,” Indonesian Football Association (PSSI) secretary general Tri Goestoro said in a statement.
“The PSSI tried to pick the best players and aimed for the best results for the last match. But Bahrain was clearly playing better and defeated us.”
PSSI national team coordinator Bob Hippy criticised Lebanese referee Andre El Haddad for awarding Bahrain four penalties and sending off goalkeeper Samsidar in the second minute.
“Before the game, I heard rumours saying Bahrain would win big and it happened,” said Hippy. “How could the referee give so many penalties for Bahrain? He killed us.”
Sports Minister Andi Mallarangeng demanded the PSSI end the infighting, which almost resulted in a FIFA ban last year.
“That is what we get if the officials keep fighting with each other,” he said.
“They should put national football’s interests first. They need to end the bickering right away. We’ve become the victims of the league’s dualism.”