Yes, but this was a lot more complicated than in the Netherlands.
During the war, the Dutch colonial government-in-exile in Australia founded the Temporal court-martials, who were tasked with persecuting war criminals and collaborators. The courts started their work as soon as the Dutch regained control over Indonesia and worked until the end of 1949.
The temporal court-marials were mainly concerned with the prosecution of Japanese war criminals. 1038 Japanese were tried, 983 where convicted, 236 were sentenced to death. Many other Japanese war criminals were sent to Japan to be tried by the International military tribunal for the Far East.
Most of the convicted Japanese were members of the Kempeitai. (De Jong 12 p. 887)
Prosecution of Dutch collaborators and collaborators of mixed descent who worked for the colonial government was limited. They were interned in camps during the war and worked for the Japanese as forced labourers, usually under appalling conditions. An amnesty was declared for people who worked for the Japanese in this manner. (De Jong 11b p. 659)
There were exceptions to this amnesty however. There is the case of the people who worked for the Japanese propaganda station ‘Radio Batavia’. The radio station sent out broadcasts targeted at Australians and Americans in an attempt to undermine morale. Material for the broadcasts was written by some Dutch journalists and some Australian and British prisoners of war. (De Jong 11b 652) There was reason to assume that some of these people were disgruntled about the pre-war colonial government and the quick military collapse during the Japanese invasion and worked for the Japanese out of their own free will. I stumbled on some reports on this case in the Dutch national archives during research on a related subject. This was not considered a major case because collaboration was not obvious and the propaganda work was really ineffective.
There is also an isolated case of police commissioner Maseland (I don’t know if he was Dutch or Dutch-Indonesian) who was guilty of betraying one of the very few resistance groups. He was sentenced to death for treason. (De Jong 11b p. 467)
The case of Indonesian collaborators was a difficult and divisive subject. Dutch hard-liners considered Sukarno himself and his entire government as collaborators and used that as an argument to defeat the republic in war and re-establish colonial control. This was also the majority view in the Netherlands for a long time. However, there was a debate about whether Sukarno really was a Japanese puppet or if he made use of his position to further his own nationalist agenda. (De Jong 11b 1046)
Most of the civil government had been run by Indonesians in pre-war times. Dutch administrators only held the top positions. During the Japanese occupation, these top positions where manned partly by Japanese and partly by Indonesians. Participation in the government was not considered collaboration in itself. In fact, the colonial government had called upon Dutch as well as Indonesian civil servants to remain at their posts after the defeat of the Allies, just as had happened in the Netherlands in 1940. (De Jong 11c p. 362) Only Indonesians who had worked for the Japanese out of conviction were considered guilty.
Not much happened in the way of persecuting Indonesian collaborators for several reasons. The post-war colonial government had no control over many parts of the country. It was hard to determine the difference between Indonesian nationalists and collaborators. It was hard to find witnesses (in contrast with finding witnesses willing to testify against Japanese). Dutch manpower and resources were strained, and were mostly allocated to the war against the republic.
There were many investigations into collaboration of Indonesians, but very few of those (if any) led to prosecution and conviction. The national archives contain many reports of these investigations, which where conducted by the intelligence agency NEFIS. These are some of the titles listed in the archives: ‘Investigation into the loyalty of civil servants, especially the NEFIS’, ‘Lists of names of women who held close relations to Japanese’, ‘Treatment of members of the NSB (The Dutch Nazi Party) living in Indonesia’, ‘About Chinese collaborators in the society Kipas Hitam’.
During the Indonesian war of independence, there have been many revenge killings of Indonesians and Chinese suspected of collaboration with the Japanese, perpetrated by Dutch, Chinese as well as Indonesians. Revenge killings against Japanese where also common. I’ve read of a case of a Japanese officer being eaten by ants.
Unfortunately all of my source material is Dutch. There may be an English translation of Lou de Jong’s monumental work ‘Het Koninkrijk der Nederlanden in de Tweede Wereldoorlog’ (The Kingdom of the Netherlands during World War 2). It’s a bit dated, and there has been a lot of criticism, but it’s still a good reference for the critical reader. Parts 11b and 12 contain the most information about this subject. There is an interesting chapter on the prosecution of Japanese war criminals.
Even in Dutch, there’s not much research into this topic. This would make quite a good subject for a new study.
Several Documents in the National Archive in The Hague (examples from http://www.gahetna.nl/collectie/archief/ead/index/eadid/2.10.17/node/c01%3A1.c02%3A1./anchor/descgrp-context-bioghist )
Lou de Jong, Het Koninkrijk der Nederlanden in de Tweede Wereldoorlog 11b, 11c, 12
Esther Zwinkels, Het Overakker-complot