Another notable, if old, train simulator from Japan is OpenBVE. It was easy to model railroads on it. Many short Brazilian routes were/are modeled in OpenBVE. It is particularly convincing since it simulates well the typical lateral wobbling that metric trains are known for.
Do you mean actual Brazilian railway track engineers used this game to plan/develop actual routes? Or just that you can play Brazilian routes in the game?
openBVE's not directly Japanese, it's an open-source re-implementation of the original BVE 2 and 4, which is.