There has been a growth in the number of Japanese startups, particularly in technology and an ecosystem of companies to support them with funding and expertise until they list on a public exchange, like the Mothers exchange.
Due to the need for expertise in IT and technology, there are more opportunities for people to join startups if they are willing to make the trade offs of working for small, growing companies. Cities like Fukuoka in Southern Japan have established programs to foster startups so there can be companies you can join there.
Depending on your Japanese ability, you can try to improve your resume with an internship before you apply a full-time job.
If you are interested in Startups, you can check out job boards like Justa.io, or an e-Commerce startup like White Rabbit Express. Some overseas sites that have companies listed are angel.co and crunchbase.
There is also a Japanese job board, Wantedly
Looking at Newspapers in Japanese like the Nikkei shimbun and Magazines like President can still be a good place to find leads. There is also specialized blogs and news websites like thebridge.jp and techinasia.
Please look at our website for past links to subjects, recruiters and let me know if you have any questions.