It wasn't so much the paint, as the way it was applied. On some Japanese planes the camouflage paint was applied direct to the airframe metal, rather than having a primer coat applied first. This combined with the often harsh climates caused the paint to flake off badly.
A6Ms usually had primer applied, as it was intended as shipborne fighter. I think the one Fencer has modelled here has had a green top finish hurriedly applied in the field.
The N1K2 is an example of an aircraft which had no primer coat applied. The undersides were left bare metal and green paint was applied directly to the top surfaces. This aircraft often flaked quite badly.