Pour the mixture into a saucepan and heat over low heat to 60°C (140°F). Maintain at that temperature for 1 hour. Remove the kombu, increase the heat to high, and bring the water to a rolling boil. Add the bonito flakes, remove from the heat, cover with the lid and leave to stand for 10 minutes. Gently ladle the bonito flakes from the bottom of the pan and discard.
Strain the stock through a fine sieve lined with an oil filter. Use immediately.