なんか難しい。。。Nihon 「ni」 ikimasu and Nihon 「e」 ikimasu, both particles can be used interchangeably after the destination that you are going. However, if you want to be exact, 「ni」is used when the destination is clear and 「e」is used when destination is vague.
Minami e ikimasu (I go south).
Conbini ni ikimasu (I go to convenience store)
Where as south can be vague as it doesn’t specify where exactly are you going, convenience store is a clear destination. In the case of going to Japan, Nihon 「ni」 ikimasu and Nihon 「e」 ikimasu are correct because one can consider Japan as a destination to be specific (among different countries, where would you like to go, A: Japan) or it can be considered to be a vague destination because you are going somewhere in Japan.