The Japanese, unlike the Germans, did not use locals to run the country. They replaced the entire system of government with their own, installed (supposedly, in effect chosen based on them not being Dutch) "natives" in junior roles.
So there were no local police, clerks, etc. etc. who could be charged with collaborating with the enemy.
They also rounded up and put in prison camps pretty much the entire local Dutch population, and any "native" who looked in the least like they were too chummy with the Dutch.
After the Japanese surrender, the Dutch had more pressing matters on hand than rounding up possible collaborators, an armed insurrection by locals which had to be put down. Paradoxically they were assisted in this by Japanese forces which had just surrendered to them, especially those were employed to continue guarding the camps housing the Dutch civilian population which had reverted from prison camps to refugee camps.
Expecting that Dutch administrators would be kept by the Japanese to run the colony, most Dutch, had refused to leave. Instead, they were sent to concentration camps and Japanese or Indonesian replacements could be found for senior and technical positions. Japanese troops took control of government infrastructure and services such as ports and postal services. In addition to the 100,000 European (and some Chinese) civilians interned, 80,000 Dutch, British, Australia, and US Allied troops went to prisoner-of-war camps where the death rates were between 13 and 30 per cent.
The Indonesian ruling classes and politicians cooperated with the Japanese who kept the local elites in power and used them to supply Japanese industries and armed forces.
Tens of thousands of Indonesians were to starve, work as slave labourers, or be forced from their homes. In the National Revolution that followed, tens, even hundreds, of thousands, would die in fighting against the Japanese, Allied forces, and other Indonesians, before Independence was achieved. A later United Nations report stated that four million people died in Indonesia as a result of famine and forced labor during the Japanese occupation, including 30,000 European civilian internee deaths.
http://japanseburgerkampen.org/vjb/cms/cms_module/index.php?lang=eng&obj_id=16196 documentary about the Japanese concentration camps for Dutch civilians during WW2.
So during the war the locals were heavily split. Those who actively cooperated with the Japanese went on to become the nucleus of the revolutionary forces that eventually campaigned to gain independence, the rest were used as slave labour and suffered horribly.
The Dutch population never noticed much about this as they were all in prison camps, undergoing hardships that made the Dachau and Bergen Belsen seem a summer vacation in comparison (I've known several people who survived those Japanese camps, their stories are horrific).