(in Occupied Korea, the Japanese at least knew that, no matter how far they went, there'd always be someone who understood Korean -- go an equivilent distance in New Guinea, and you'd run into languages as different from one another as Ubykh, Navaho, and Swahili. I probably fail at imperialism, but what's the point in having a subject population who can't understand what you're telling them to do?)
Their were parts of Africa that did'nt even know they were colonies of the European powers, so I don't think it's that much an issue.
New Guinea would be important for its coastal areas initially, eventually the Japanese would gradually move in and both teach Japanese to the groups that they could get translators for as well as just force the rest to learn it, much as America did with Native Americans.