Submitted PR application and then filed income tax late, how screwed am I?

Background: I applied for PR recently (before March 15) after 1 year of moving to Japan with the 80 points calculation. Because I hadn’t paid national income tax or residence tax yet, my record was squeaky clean with all other payments handled by my company. I have a 5 year Engineer visa and working at a FAANG company.

The unfortunate part: Because I receive RSUs and taxes were handled by a tax accountant this year, I still had to file that part of the tax return, and mistakenly assumed this would automatically be deducted from my bank account as I had given the accountant that info. They filed my taxes but I was still responsible for manually taking the prepared slip and going to the tax office to pay. Long story short it’s still my mistake for not following through and going to the tax office, and one day I received an intimidating letter from the tax office saying to pay up. Of course I paid up immediately the next day and feeling incredibly regretful.

I would like to know if anyone has been in a similar situation as mine and what the result of their PR was? My PR app probably hasn’t even been looked at yet by immigration but I have these two options I could take:

1. Submit a letter of explanation preemptively explaining this whole situation and emphasize this mistake will never happen again and attach it to my application now.
2. Wait until immigration starts processing my application, see if they investigate this further and ask me for additional docs/interview to explain my situation. In which case I will provide them with all the docs they ask for then.

When I spoke to the tax office, the staff said that the tax certificate, namely the 納税証明書(その3)which is the one to submit for PR will not show any late payment. I’ve probably read every post about PR on Reddit in the last few days and it does seem overwhelmingly stacked against me. I was that person that was always so careful to reread these documents and was certain I wouldn’t pay any taxes late, but of course I made one of the biggest screwups possible for my PR chances. I’m fully aware I can reapply again. Hoping I can get some anecdotal evidence and advice here from people successfully getting PR despite this just because the PR wait is brutally long, so it will give me some peace of mind until then.

by AlbinoCherryTomato

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