Never let your visa application stop you from traveling.
You can go to Japan Immigration Department to lodge an appeal. You will need to write the reasons why your case needs to be heard and provide pieces of evidence that support your explanation letter.
The immigration officers will review your evidence and decide whether your application should be heard and go on back to the normal process.
Note that you can only lodge an appeal if your visa application was applied onshore. Tourist visas in most cases cannot lodge an appeal but you can reapply after six months.
What will happen if I reapply within the six-month period from the time it was rejected?
According to Japan’s Foreign Affair’s website, your visa will be denied if your previous visa application was rejected and you reapply to visit Japan for the same purpose within six months from the rejection. This is because the circumstances of the applicant would not change and that the result of examination would be the same.
Can I apply within six months from the rejection but with a different purpose?
You can definitely apply again with different purpose. This time, make sure to submit proper documents to avoid visa denial. In most cases, denied applicants can still get a visa by applying a different purpose of travel such as with guarantor letter or travel for humanitarian reasons.
You may consult the nearest Embassy or Consulate if you think you need more detailed advice about your case. In the Philippines, you can visit the nearest accredited agencies where you plan to apply for the visa before making the application.