Things are not going well in your relationship, and your Japanese partner is threatening not to sign your Spouse or Permanent Resident visa application.  Of course after that, they may divorce you and run away with your child.  Here is some advice if you are living in Japan already

If you have not been living in Japan for 6 months yet, leave.  Get out.  Although Japan has not ratified the Hague Convention on International Child Abduction, 6 months is the generally accepted time required to establish habitual residency. Some countries like the UK, reportedly treat Japan as if they had really signed this convention, and might return you to Japan.  Its gravely unfair to the non-Japanese parent as Japan will not treat their own citizens the same way, so check.  But another parent who went to the UK to flee spousal abuse was able to stay with their child.  So it may depend on how you position it.  But some do not, like often in the US.  See the foreign law cases and the success stories for situations when a parent, even one who had been living in Japan for some time, was able to leave, and the courts let them stay because of the situation with Japan.  Once you are out, you can negotiate a divorce and child custody from a position of safety and equality.

CRN Japan does not endorse parental kidnapping of children.  But in this situation, your child having been in Japan for over six months, you have a problem.  You may have to leave, yet your child, a Japanese citizen, may have to stay.  In fact, even if your child has dual citizenship, your spouse may be able to force them to stay since they also have dual citizenship.

Finally, after reading this section, be sure to see the section on Afraid Your Spouse Will Abduct Your Children and Afraid Your Spouse Will Divorce You.  Also see the section on Japanese Visas.

The following is VARIOUS NOTES FROM EMAILS ON THIS SUBJECT that needs to be incorporated into this page.

You might be able to start with a LT (long term) visa as a custodial parent, but the PR visa still has a time requirement attached (5 years if you are married, 10 years if you are not). And I think there have been cases of custodial parents not getting the visa even though they were eligible and applied. I'll try to dig something up on this. I know I read something, but I'm not sure I archived it.

I have been looking into the custodial parent visa because the parent of my child  is Japanese. I can apply for an LT visa (3 year limit) as the custodial parent of a Japanese citizen with reasonable expectation of it being granted. And once I've completed my 10 years successive residence under valid visas I can then apply for PR. On the other hand I just received another 3 year working visa which will put me right on the cusp of the 10 year requirement to apply for PR. There is one very big advantage of an LT over a working visa. It is not tied to a specific job or job category.

Presently people who are forced to leave Japan and really want to come back do so by legally changing their name and getting a new passport. Soon this will no longer work, since they are going to have retinal identification systems set up in immigration control areas of travel hubs.

The use of immigration law to get Ken Massey "out of the way" is precisely one of the things that is so annoying about Japan regarding it's treatment of foreign parents of Japanese nationals. He had the chance to get PR status, but he was ignorant of its importance until it was way too late. There should be some leeway that allows for a sort of retro-active chance to apply for PR if one was qualified for it, as long as no other crimes harmful to society have been perpetrated. Ken Massey was not a criminal as in "dangerous" or "harmful to society". He was just an ordinary hard-working taxpayer who had the wrong nationality. He got totally screwed, because he had no network in his country of origin after 17 years in Japan.

If you've been in Japan 10 years, you can get permanent residency without being married. But you still need a sponsor. And your sponsor does *not* need to be Japanese. Your sponsor can be someone with permanent residency. I know this because I once sponsored a good friend for permanent residency. It was an easy and simple process on my part.  So another option might be to get some kind of sponsorship via working for a company for another year, then apply for permanent visa using sponsorship other than your wife.

I was separated from my wife and living in a different address, which I used on the application for the permanent visa. Immigration called me and asked why my address was different than the address of my wife. Permanent residency was denied. Fortunately, I already had a work visa.

If you can't work things out I suggest making her sponsoring you for permanent residency a condition of you agreeing to a divorce (and only agree to the divorce AFTER you have your PR status).  A divorce is your only leverage.

Now for some advice - if you want to get back together with your  wife you need to do one thing and one thing only - understand her perspective on what went wrong and do EVERYTHING humanly possible to show her that you are correcting that. Reality has nothing to do with it.

You don't sound so lucky. I would suggest that you find one of her friends who is, if not sympathetic to your cause, at least indifferent to you.  Tell that friend that you desperately love your wife and want to make whatever it is right and ask them to play the part of an intermediary between the two of you, but being a dense male you have no idea what the problem is could they please help. Then listen to whatever the friend says, do not argue, do not try to impose your view of reality onto the situation, accept that this is her reality and what you are going to have to make right. Then do WHATEVER IT TAKES to make it right!

<TODO: Add a special section on what to do if spouse or child abuse is occurring. Perhaps on main menu under Help Now...>