Here are links for those are in Japan and want to donate through Japanese or Japan-based organziations.
When donating to solicitors of the street corner donation groups here in Japan, be careful. From one Japanese contributor: “Be wary of some of those on street corners and at train stations. A good method of checking if they’re legit is to ask where their donations are going, as well as what organization they represent. My daughter saw a couple of teens with a cardboard box and they ran away as soon as she asked.
One thing to remember about donating directly to any Japan-based relief organization from abroad is that the exchange rate weighs heavily against those people outside Japan. It is probably in your best interest in terms of how far your money goes to donate to your local relief organization and let them handle it from there.
(donating to the Japanese Redcross Society involves going to the bank and depositing money through a bank transfer. Please remember these require bank fees. Also please remember that the exchange rate at the moment is most likely not in your favor if you are outside Japan)
“Second Harvest Japan distributes food to soup kitchens, orphanages, the elderly, emergency shelters, single mothers, the homeless, migrant workers, and many others. Second Harvest Japan は、生活に困っている人々と彼らの支援団体を食を通じてサポートしている特定非営利活動法人（NPO）です。”