I live in Japan and while also not a lawyer I've had experiences with the labor bureau - this is totally false, and even explicitly stated in the Labor Standards Act:
"Article 5: An employer must not force a worker to work against their will through the use of physical violence, intimidation, confinement, or any other means that unjustly restricts that worker's mental or physical freedom.
...
Article 16: An employer must not form a contract that prescribes a monetary penalty for breach of a labor contract or establishes the amount of compensation for loss or damage in advance."
(Source: https://www.japaneselawtranslation.go.jp/en/laws/view/3567)
This explicitly applies to contract workers (契約社員) too, and protections for employees (正社員) are so strong that it can often take months of documentation to dismiss someone. Whether people know they have these protections, knew they had them before they sign something their company gives them or feel comfortable actually reporting when a company has violated them is a different story. But basic salary is protected strongly enough that most Japanese companies heavily weight compensation on annual/semi-annual bonuses, housing allowances etc... (which are not protected).