Samkvæmt Nintendo Japan <a href="http://www.nintendo.co.jp“>www.nintendo.co.jp</a> hefur Metroid Prime verið breytt lítillega fyrir japanskan og evrópskan markað. Hann hefur verið gerður erfiðari, fleiri items bætt inn í hann og fleiri cut-scene og jafnvel eitt alveg breytt cut-scene.

Það er þó nokkuð öruggt að þessi nýju items eru ekki hlutir sem geta haft áhrif á leikinn, líklega bara fleiri bomb capacity upgrades og energy tanks.

Lausleg þýðing af nintendo.co.jp (tekið af IGN gameboards):

”Unusually, the difficulty of the Japanese version is higher than that of the American version, although it is the same as the version released in Europe. Also, in the European and Japanese version of the game there are a greater variety of items. Some of the cinemas have been changed. More specifically, certain effects have been added, and some animations have been changed. There are cases when a completely new cinema has been added, in particular, the Grappling Beam."