For most of the war Ki-43s left the factory in bare metal, with only an anti-glare panel and red hinomaru markings in six positions. Camouflage schemes were painted in the field without primer and with whatever paint was available. Late in the war a factory-applied camouflage scheme was introduced, olive green on top with grey below. I'd guess this was because of the increased risk of Allied bombing or interception before the aircraft even reached their units. As far as I know this was also the case with other IJAAF fighters like the Ki-44, Ki-61 and Ki-84, although I haven't researched that enough to be sure.
For the IJNAF the situation was reversed. A6Ms were always well painted, probably due to the increased corrosion associated with carrier ops, but later fighters like the N1K2 had camouflage paint applied to the bare metal and to the upper surfaces only.