Pahang arrived in Jakarta on Saturday, but were left stranded at the airport after Nigerian striker Dickson Nwakaeme, Jamaican defender Damion Stewart and Pakistani defender Zesh Rahman were detained for not possessing a visa.
While Pahang's FA manager Fahrizal Hassan was livid with the Indonesian Football Association's (PSSI) "incompetence", he pointed out that "there’s nothing much we can do since [the] AFC have not made any decision".
"The rule book says that we should be given a walkover, but we’ll have to wait for AFC to decide on the matter," he told The Star.
Fahrizal added that he was astounded the PSSI didn't do anything to help the players, who spent Saturday night at the airport before returning back to Kuala Lumpur on Sunday morning.
"It’s ludicrous to be in this situation in this modern era," he said. "We did everything we could to play against Persipura but were let down by PSSI’s incompetence.
"Our officials have met their Persipura counterparts in Jayapura and explained our situation … they seem to understand our predicament.
"I hope we can get an answer from AFC soon so that we can prepare for our next course of action."
The Asian Football Confederation (AFC) are aware of the situation and confirmed that an investigation has been launched.
"We are in the process of gathering information from all relevant parties," a short statement on the AFC website said. "Once the investigation is concluded, a report will be submitted to the appropriate AFC committees for a final decision."