The fine is a maximum of 500,000 yen and it counts towards your criminal record for things like PR application.
The law is 統計法 第61条第1項(+第1号)
Which states:
次の各号のいずれかに該当する者は、五十万円以下の罰金に処する。
第1号
第十三条の規定に違反して、基幹統計調査の報告を拒み、又は虚偽の報告をした個人又は法人その他の団体（法人その他の団体にあっては、その役職員又は構成員として当該行為をした者）
A person who falls under any of the following items shall be punished by a fine of not more than 500,000 yen.
Item 1
An individual, corporation, or other organization who, in violation of the provisions of Article 13, refuses to report for a fundamental statistical survey or makes a false report (in the case of a corporation or other organization, this applies to the officer or member who committed the act on behalf of the entity).
by ToTheBatmobileGuy