World governing body FIFA appointed a so-called 'normalisation committee' in April to organise the election for the PSSI following chaotic scenes when opponents of former chairman Nurdin Halid broke into the election meeting.
Halid was jailed in 2007 for misusing funds but continued to run the PSSI from his cell.
On Friday the head of the normalisation committee stopped the meeting after six hours as rival sides tried to grab the microphone and over three-quarters of vote holders demanded nominees banned by FIFA be included in the contest.
"Because the situation is no longer conducive and it's impossible for us to come up with an outcome, by saying thanks be to God and my deepest apology to the people of Indonesia, I state that the congress is halted," said Agum Gumelar, the committee head.
The abrupt closure of the meeting without a decision sparked more shouting and protests while security officers jumped on the stage to try to protect the committee and a FIFA observer.
The barred nominees are George Toisutta, an Indonesian army general, and Arifin Panigoro, a wealthy businessmen.
Both were banned after FIFA pressure for involvement in launching a breakaway Indonesian League (LPI) which attracted teams from the PSSI-supported Indonesia Super League (ISL).
Gumelar told Reuters that it is unlikely the congress would re-open.
"For now we will just wait for FIFA's decision," he said. "They sent an observer who could see the situation with his own eyes."
The developments could jeopardise Indonesia's participation in the 2014 World Cup qualifying rounds should FIFA decide on a suspension.
Indonesia, ranked 130th by FIFA, have been drawn to play Turkmenistan in the second round of Asian qualifying, with the first leg to take place on July 23 in Ashgabat before the return in Jakarta five days later.
Despite a huge football-mad population, Indonesia's only World Cup appearance was in pre-independence days in 1938 as the Dutch East Indies and is not recognised by the PSSI.
