From East Timor: The main crossing is at
Mota'ain between Batugade in
East Timor and Atambua,
West Timor.
From Malaysia: The only formal way to enter by land from Malaysia is at the
Entikong-Tebedu crossing between
West Kalimantan and
Sarawak,
Malaysia on
Borneo. The crossing in on the main route between
Kuching, (
Sarawak) and Pontianak, the capital of (
West Kalimantan). As the crossing is listed only as a visa-free entry point, nationalities who do not qualify for this will have to apply for visas beforehand.
From Papua New Guinea: The only recognized crossing into Indonesia is at
Wutung, between
Vanimo in Sandaun Province in
Papua New Guinea, and
Jayapura, the capital of Indonesian
Papua.
Note: It is not guaranteed that you will be able to enter Indonesia through these crossings and non-Indonesians are required to apply for visas at the nearest Indonesian Embassy or Consulate.
New Zealand