Two gunmen barged into the house of Muammar Biston in Sultan Kudarat town and shot him as he was praying.
Police chief Dicalingan Maslah said a driver of the victim was also injured in the attack, but two other relatives of Biston were left unharmed.
Biston was one of the religious leaders of the MILF. No motive for the killing could be immediately established, Maslah said.
Salamat, the MILF’s founder and chairman, died in July from complications from a heart ailment and an acute ulcer.
Talks are expected to be held in Malaysia later this month after plans were put on hold during the observance of the Muslim holy month of Ramadan, which ends next week.
Before his death, Salamat renounced terrorism, one of the key demands made by the government for the resumption of talks to end the decades-old Muslim armed struggle for a separate homeland in the country’s troubled South.