Employer gave me a raise then tried to cut my salary a week later – advice needed

I'm a Brazilian national working as a 正社員 (permanent employee) at a small company in Yokohama. I've been here about 10 months and although I never really liked the job much, things have taken a difficult turn recently.

On March 31 my employer and I both signed a salary revision contract increasing my pay. The previous day I had been late due to a verified train delay, so I submitted the official lateness certificate (遅延証明書) per company procedure and the lateness was reversed. The following morning I was again late due to another train delay and followed the same procedure. However that morning the company president (社長) publicly confronted me in the morning meeting with my team, privately threatened me with dismissal, and then demanded the return of the signed salary revision contract. Due to the power imbalance and the dismissal threat I felt unable to refuse, but I took a photo of it for assurance.

One week later I was presented with a new contract reducing my salary – and not just the allowance part of it, but also the base salary. The reasons given verbally, other than the one instance of delay on the previous week, were smartphone use – which I used at the start of my tenure in the company to do things such as taking notes during meetings – and long toilet breaks – due to occasional but recurring constipation issues that I have. Both of these issues had only existed months before the raise was given, and were addressed after feedback from my team, with the last warning on those having happened over five months ago. The company was fully aware of them when they gave me the raise. Nothing changed between the raise and the cut except the train delay incident. The pay cut contract itself contains no written reasons – everything was communicated verbally only. I have not signed it and do not intend to do so.

My company's own handbook explicitly exempts lateness due to unavoidable reasons from discipline and there is an official process for justifying lateness. A colleague has been repeatedly late due to train delays across multiple months with zero consequence – I have the emails to prove it. The company president verbally admitted different standards apply to me versus this colleague due to contract type, me being permanent while him being some other type of contract, but he still has to report when he is late, which is fishy. Not only that, but the company has a rule stating that three instances of delay below 30 minutes or one instance of delay over 30 minutes means either a whole day of vacation is discounted OR the pay of a whole day is docked, which seems to be clearly illegal as the laws limit punishments of this sort to half a day of salary and does not permit reducing PTO without employee consent.

I visited the labor office (外国人労働者相談コーナー) who confirmed the company's rules above regarding lateness above violate Japanese law, and assessed the company as having an authoritarian (ワンマン) president likely to refuse mediation through them, though they also said they would not know for sure until they tried. I also consulted a lawyer, who outlined a demand letter approach, but noted that direct awards may be too low to justify a case without dismissal, which is complicated for me when he has a 230000 yen retainer. My payslip date is April 25 and I expect the company may implement the deduction without my consent. Yesterday I sent a formal email to HR (総務) explaining my reasons for refusing to sign and asserting the March 31 contract terms continue to apply, but who knows what is gonna happen out of all of this.

I have documentary evidence of all of this including official attendance data in XLSX format, EML email files and screenshots showing the colleague's repeated unpenalized lateness, Mattermost search results confirming no warnings about the stated reasons for the reduction after the November informal message, a photograph of the signed salary revision contract, and the unsigned pay cut contract as well.

I would be very grateful if anyone would have any advice as to what measures to take regarding this situation.

Update on this: the president called me to talk today after reading the e-mail and, as expected, did not take it well at all, insisting that I am in the wrong and that my workmates will back his points. He wants me to resign, but I refused and told him to take the appropriate measures if he thinks that is better.

Looks like this is shaping up to be a legal battle, indeed, rather unfortunately.