Koji is thought to have been first produced by the "natural fermentation starter method" using mold which grew naturally on grain. Next, the production method is thought to have shifted to the "Tomodane method" where koji that was produced in good condition by chance was then saved and used as the next starter. Of course, the "Tomodane method" was very unstable in terms of quality, and was not the ideal method for Tane-koji(seed koji). During the Muromachi period (1333-1573 CE), it was discovered that when koji was cultured mixed with wood ash and used for the next koji production, there were fewer failures. This became the foundation of the current day Tane-koji(seed koji) method. Recent studies have shown that the scientific basis for using wood ash in Tane-koji(seed koji) production is that wood ash suppresses the bacterial growth, and molds other than koji mold (Aspergillus) and improves the durability of the Aspergillus spores. Regarding the effect of wood ash, a very interesting experiment carried out by Takeo Koizumi, Professor Emeritus of the Tokyo University of Agriculture, is described below.
When rice porridge is left indoors for about 3 days, various molds such as red, green, black, white and yellow mold grow. The area where the mold formed was extracted and ash produced by burning sawtooth oak was lightly sprinkled over the mold. Each day, a small amount was collected from the surface and dried. This was performed for 12 days, resulting in 12 samples. Each of these 12 dried samples was separately sprinkled over steamed rice to make koji. Koji made from the samples showed mucor, red mold and green mold from the Day 1 to Day 3, and almost no koji mold. However, koji mold gradually appeared, and from Day 10, only koji mold could be seen. From this, only Koji mold which has strong resistance to ash could survive, and other molds were culled out.
According to this, using wood ash during koji production was a very good method to separate koji mold. However, since this method remained a secret, and only members of the "koji guild" were permitted to produce Tane-koji(seed koji), and Tane-koji(seed koji) was produced by only two companies, this company and one other (both located in Kyoto) until 200 to 300 years ago.