The best way to begin freelancing in Japan is to just start doing whatever it is you do — as long as this is allowed under your visa. You’ll need to obtain a "Permission to Engage in Activity other than that Permitted under the Status of Residence previously granted" from the Immigration Office, but essentially, the first step to going freelance is to just DO it. If you wish to continue with your current field of business but move into freelance, then you will not need permission to engage in the same activity, but you will need to self-sponsor your visa or be sponsored by one of your regular clients.
Legally, it’s up to you to make the appropriate enquiries to find out if the activity you plan to do is permitted under your current visa. Generally speaking, foreign residents who are sole proprietors will have either an "Engineer/Specialist in Humanities/International" visa (hereinafter, Humanities visa), or a "Business Management" visa, unless they are on a permanent resident visa.
See more about the visa types you want to consider as a freelancer:リンク