Six passengers were also wounded in the burning of the bus in M’lang town in Cotabato province, some 950 kilometres south of Manila, on Thursday, a police report said.
Investigators said three male suspects set the bus on fire using "a highly combustible liquid substance” along the national highway.
The three fatalities - two women aged 28 and 30 years and a man aged 18 - were trapped in the bus.
The other passengers escaped by climbing out of a window at back of the bus, the police report said.
Police said investigators were looking at extortion as the possible motive for the attack, noting that the bus company had received demands from criminal groups in the town. - dpa