The Indonesian Football Association (PSSI) called off the congress after opponents of chairman Nurin Halid, who was jailed in 2007 for misusing funds but continued to run the organisation from his cell, claimed they had been stripped of voting rights.
Around 20 members of a reformist group stormed the meeting in the Sumatran city of Pekanbaru after finding they were not on the list of 100 delegates eligible to vote on the election process, forcing the event to be cancelled within minutes.
The PSSI maintain the protesters did not have voting rights to begin with and felt the only course of action was to call off the congress after just 20 minutes as it was impossible to continue.
The organisation's general-secretary Nugraha Besoes explained to a hastily arranged media conference that PSSI, FIFA and the Asian governing body (AFC) representatives agreed to halt the congress after a brief consultation.
"It is impossible to continue the congress," Nugraha told reporters.
"What we all saw there is embarrassing for the organisation and the country."
Nugraha added that it was down to FIFA to decide "what to do next" and hoped the world governing body would not punish them too severly for the commotion.
Association officials, along with FIFA representative Frank van Hattum and AFC secretary-general Alex Soosay, were on their way to the venue when they witnessed the row taking place.
"When they saw the situation in front of the hotel, they said that we couldn't hold the meeting under these conditions. We had to cancel it," Nugraha said, without indicating when a new general assembly would take place.
"That's when we decided to turn back and return to the airport and hold a meeting there."
