Police accused Masashi Yokouchi, 33, and four other suspects for the sale of the illegal drugs via six sites, including Skull 69 Tokyo, from an office inside an apartment in Yashio City, Saitama Prefecture.
A search of another apartment that served as a warehouse in Kawaguchi City revealed 700 packages of 50 different types of contraband.
Dangerous drugs are sold in packets as a combination of chemicals whose structures are often able to exploit legal loopholes and organic material.
Four of the suspects, who have been charged with violating the narcotics control law, have denied the allegations while one has admitted to the charges.
Skull 69 Tokyo offered 24-hour ordering and free delivery within the 23 wards of Tokyo for purchases over 10,000 yen.
Since January of last year, sales through the sites have totaled more than one billion yen. Police believe that the accumulated sales through the sites operated by the suspects account for more than half of the nationwide dangerous drugs market.