Open nameko package and rinse them in running water. Drain.
Remove tofu from the package and cut into small cubes (a little bigger than dice size).
Place nameko mushrooms in a small pot. Add mirin, water, soy sauce and bonito flakes. Mix well and bring to boil over medium heat, stirring occasionally.
Reduce heat to low and add tofu. Cook for additional 3 minutes. Stir gently.
Garnish with scallions to serve.