Can I leave Japan while waiting on a visa?

My "spouse of (a) Japanese national" visa expired early in summer. I applied for a new one early in July. In my memory, the postcard informing you that your new visa is ready, comes quite quickly. Thus I thought that I would have it by the time I booked tickets to Ireland (which I booked at the end of July). I didn't. So I rang the immigration to ask the question: "Can I leave Japan while waiting on a visa?" Their answer was yes. Just to be sure, my native Japanese husband also rang and confirmed that it was okay for me to leave Japan while I was waiting on my new spousal visa.

What they neglected to tell me was that, while there is no law against you leaving, it nullifies your visa application. The postcard to say that my new visa was ready to pick up arrived while we were in Ireland. On the Monday after we got back from Ireland my husband and I went to the Tokyo Regional Immigration Bureau Saitama Branch Office. I had the four things they required with me: the postcard they'd sent out, my old alien registration card, passport and a revenue stamp of payment. All ready to pick up my new visa... or so I thought.

After an hour of waiting, after handing in the four items, my name was called over the intercom. My heart sank. I knew something was wrong, because they rarely call anyone by name - they use a numbered ticket system and they call the number. I raced up to the desk. The attendant told me that they could not give me the visa, because I had left the country after applying for it and it was no longer legal / valid.

It might seem like a strong word, but I was devastated. If your immigration office is as busy as ours, you'll understand why! It is such a chore applying for the visa and the wait in the immigration office is soul crushing. And I have to do it all again. Including getting and paying for new copies of the family register and resident record. Presumably because I left the country, albeit only temporarily.

I asked her 'seen as I have to do it all again from scratch' could I apply for permanent residency instead. She said no, because currently I am on a regular 90 day tourist visa and you can't apply for permanent residency on a tourist visa. Thankfully I still have another 70-odd days to reapply, because with the trauma of the experience still lingering I am no more in the mood to hang around the Immigration Office for at least half a day in the near future!

So yes, you can leave Japan while you are waiting for a new visa, but it nullifies your application and you will have to reapply for the visa when you get back to Japan.