The relevant legislation is here (in Japanese). This is only for Tokyo, the legislation in all other prefectures is similar but may differ in some details.
Basically, it's "illegal" for parents to allow a minor to go out between 11pm and 4am except for going to work/school or for some other "justifiable reason". What constitutes a "justifiable reason" is as usual unspecified and left to the judgement of police officers/judges/etc. I put "illegal" between quotes because the ordinance says you must not do it but it's not clear what the penalty is, if any. It's also not clear if hotels are considered "home", so it's possible that he will technically be out of his home anyway.
Edited to add : there is a difference in interpretation between jpatokal and I, so here is mine in more detail. jpatokal correctly translates clause 1 as saying that a parent must not allow a minor out between 11pm and 4am without a "good reason". However, in his commentary below his translation, he adds "by themselves". As far as I understand the Japanese text, there is no reason to add this, and clause 1 applies equally no matter by whom, if anybody, the minor is accompanied.
Clause 2 forbids anybody from accompanying a minor out without a "good reason" or parental consent. Presumably, the bar for a "good reason" is higher here, since it allows anyone to take a minor out without parental consent, maybe even despite parental oposition in extreme cases. In normal situations, however, parental consent is required, and by giving it without a good reason, parents violate clause 1.
Other edit : I will also add that the bar for a "good reason" in clause 1 is probably quite low. Yesterday at about 11:30 just after first posting this answer, I went to the convenience store to grab some late night snacks. There was a boy probably no older than 10 with his father also buying stuff, and the staff didn't say anything. So being hungry and needing to buy food probably qualifies. (I am not in TOkyo, but the law where I live is similar.)