Yes, it's easy. Use a custom Scene_Items scene and set CUSTOM_SCENE_ITEMS (or soemthing like that >.<) to true.
@Twinn Killa: There is an array which says "$quest_items = [NUMBER1, NUMBER2, ...]". Simply add item IDs into that array and separate them with commas. The items with those IDs will not appear in the normal item menu, but in the Quest Item menu instead. Basically what Nortos already said.