For much of the war most IJAAF fighters came in bare metal finish from the factory, with just the anti-glare panel and national markings painted on. Any camouflage paint on the upper surfaces was done at a depot or unit level. Around mid-1944 the IJAAF instructed factories to start painting the aircraft in an olive brown and grey scheme. This was because the homeland was coming under threat of aerial attack and there was a risk of new aircraft being attacked on the ground or as they were being delivered.
For instance Ki-43 I and IIs were built in bare metal, but the IIIs which began to arrive in 1944 were all factory painted. I suspect something similar happened with the Ki-61. Photos of Ki-61-I variants I have seen all seem to all have been bare metal while the Ki-61-II and Ki-100s appear to have factory painted schemes. I've not found a written source to confirm this though and its possible some late Ki-61-Is were factory painted as well.
