Indonesia is an interesting place.
Its a federation so each 'state' thinks it can make its own lawys. Each island thinks its independant from each 'state' so they think they can make their own laws. As there are 13,000 islands who all think Jakarta is a looong way away, there are many different laws
We found a town that was a port of entry when we were trying to clear out. Its surprised the officals that they were an official port of entry and so it took 2 days to clear us out. Mind you it took 4 days to clear us into indonesia and that was with the admin support of a 130 yacht rally
You need your visa prearranged in darwin.
I thought the closest port of entry was in Indonesian Timor at Kupang. By often accounts a place of interesting officials!
Noonsite: Indonesia
another source says:
Seaports
1 Bandar Bintan Telani Lagoi in Tanjung Uban, Bintan (Sumatera)
2 Bandar Seri Udana Lobam in Tanjung Uban (Sumatera)
3 Citra Tritunas (Harbor Bay) (in Batam, Riau Archipelago)
4 Belawan in Belawan (North Sumatera)
5 Benoa in Bali (Island of Bali)
6 Bitung in Bitung (Sulawesi)
7 Jayapura in Jayapura (Irian Jaya)
8 Marina Teluk Senimba (Batam Island)
9 Maumere in Flores (East Nusa Tenggara)
10 Nongsa in Batam (Batam Island)
11 Padang Bai in Bali (Island of Bali)
12 Pare-pare in Pare-pare (South Sulawesi)
13 Sekupang in Batam (Batam Island)
14 Sibolga in Sibolga (North Sumatra)
15 Soekarno-Hatta in Makassar (South Sulawesi)
16 Sri Bintan Pura in Tanjung Pinang (Riau)
17 Tanjung Balai Karimun (Sumatera)
18 Tanjung Mas in Semarang (Central Java)
19 Tanjung Priok in Jakarta (Capital of Indonesia)
20 Teluk Bayur in Padang (West Sumatra)
21 Batam Centre in Batam (Batam Island)
22 Soekarno-Hatta (in Makassar, South Sulawesi)
23 Yos Sudarso in Dumai (Riau Province, Sumatra)