In September, the headline annual inflation rate rose to 5.95%, up from 4.69% in August.
The annual core inflation rate, which excludes government-controlled prices and volatile food prices, reached 3.21%, compared with 3.04% in August and 3.6% forecast by analysts.
The September inflation was mostly affected by the rise in fuel prices and inflation in the transport sector, said Margo Yuwono, head of Statistics Indonesia.
He warned that it could heat up further in October as a number of regions have not yet increased their transportation fares.