It’s very rare for companies in Japan to explicitly recruit “Junior Developers”, so if you’re just getting started with your career you’ll most likely need to apply for positions that require “3+ years professional experience”, or something to that effect. You’ll be facing an uphill battle with getting interviews with them, as by default they’ll assume you’re under-qualified.
To overcome this, you’ll need an exceptional application, that demonstrates you’re more than just someone with a Comp Sci degree, but actually will be able to bring value from day one. Create something explicitly tailored to the given company, rather than a generic application you copy and paste from one to the next. It’s my impression that applying to smaller startups works better for this, as you’ll have a higher chance your application will be screened by someone like the CTO themselves, who can choose to make an exception to a policy, rather than a HR person who will bin your application because you don’t match their list of requirements.
For more on this, I’d recommend the book Hired Fast. I thought it had some good examples of how to make yourself stand out.
I also highly recommend How to write a Developer CV/Résumé that will get you hired, as it gives some concrete tips on how to compellingly highlight your skills.
One thing you didn’t mention is your Japanese ability. If you speak at least a conversational level, you could try approaching Japanese startups who aren’t explicitly recruiting international devs on Wantedly. Because they won’t be getting applications from people like you, there’s a greater chance that you’ll at least be able to land an interview out of curiosity on their part.