Six of the 11 PSSI executive committee members met on Wednesday and opted to remove Halim Mahfudz and replace him with Hadiyandra, the Jakarta Post reported.
"The (PSSI) chairman (Djohar) said he could no longer cooperate with the former secretary-general," executive committee member Tony Apriliani told the newspaper.
Indonesian football has been ripped apart by the fighting between the PSSI and the Indonesian Soccer Rescue Committee which resulted in the populous southeast Asian nation having two domestic leagues and two national teams.
FIFA have long threatened Indonesia with punishments and bans if the row was not resolved with the latest deadline being extended to March 20.
The rival factions have agreed to hold a FIFA requested joint congress in Jakarta on March 17 to try and move forward as one.
Bob Hippy, an executive member who did not attend Wednesday's meeting, said the sacking of Mahfudz was an "illegitimate" decision.
Hippy said four of the members present in the meeting were yet to be officially reinstated after they had formed the breakaway KPSI, arguing that they could only be ratified at next month's congress.
Nevertheless, Hadiyandra said he would press on with the role.
"I will send a letter to FIFA to clarify the status of the congress, whether or not it is an extraordinary congress," he said.