Pahang decided to leave Indonesia after the team's foreign players were denied entry due to visa problems.
The setback occurs just a day before Pahang are scheduled to face Persipura in the first leg of their last 16 clash.
Pahang FA honorary-secretary Fuzeimi Ibrahim was infuriated upon hearing the news and blamed the Indonesian Football Association (PSSI) for failing to sort out visas for the team's foreign players, which include Nigeria's Dickson Nwakaema, Jamaica's Damian Stewart, Pakistan's Zesh Rahman and Argentine Matias Conti.
Ibrahim also claimed that all visa applications had been submitted to the Indonesian Embassy in Kuala Lumpur on May 18.
"We were promised that everything will be sorted out and the players will be issued visa on arrival," he told the New Strait Times. "Sadly, the players were left stranded at the airport (Jakarta International Airport) and Pahang FA decided to return home.
Ibrahim added that he would be lodging a complaint against the PSSI via the Football Association of Malaysia and the Asian Football Federation (AFC).
"We will lodge an official complaint to the Football Association of Malaysia and the Asian Football Confederation (AFC) on Monday," he said.