
These are species with at least one recorded territory in Indonesia, not a national checklist: a bird list from eBird or Avibase is more complete. The counts follow recording effort as much as wildlife, so a country with more visitors and more naturalists will show more of both.
The species with the most open occurrence records in Indonesia, among those a photograph exists for. Most recorded is not most numerous: it rewards animals that are common, conspicuous and live where people go.

Collocalia linchi

Pycnonotus goiavier

Todiramphus chloris

Collocalia esculenta

Passer montanus

Cinnyris jugularis

Haliastur indus

Ardeola speciosa

Hirundo javanica

Icthyophaga leucogaster

Lonchura leucogastroides

Geopelia striata
The reference database has no regions filed under Indonesia.
The field guide covers Indonesia on the map, but none of its species have an entry written for them yet.