At the time of national entry into Japan, the original PCT and its Japanese translation must be filed, and any other amended version except the amendment that was made under PCT article 19th or 34th at the international stage cannot be submitted. Then applicants can file a voluntary amendment anytime thereafter, typically in conjunction with filing a request for examination.
Please note that if you have an allowed set of US or European claims for example, you should file your amendment before or in conjunction with filing a request for examination. In Japan, amendments made after receiving the first office action that are replacing a currently pending claim set with the new one would undoubtedly be deemed as the so-called "shift-amendment". If the application were deemed as "shift-amended", it would then inevitably be rejected without being put under further substantive examination, whether the claims as amended are objectively patentable or not. So our associates strongly recommend forgoing replacing the claim sets after the first office action in order to prevent things from getting harsher.