Transportation began Tuesday morning of 120 kg of the radioactive mineral monazite from a computer store in Omiya, Saitama Prefecture, to a research center in the prefecture.
The monazite, detected in about 90 drums in a store warehouse in Omiya, will be moved to the Institute of Physical and Chemical Research in Wako, an affiliate of the Science and Technology Agency.
Monazite contains thorium and uranium, and possessors must report to the government if they hold amounts exceeding a government-set limit.
The 120 kg of monazite was part of 20 tons of the material found stored in various locations in Chiba, Saitama, Ibaraki, Nagano, Mie and Gifu prefectures, as well as in Tokyo, since June.
Its existence came to light after a total of 30 grams of ground monazite was mailed separately to 10 governmental bodies, including the Prime Minister's Official Residence, in early June.
Police found the 20 tons of monazite in a series of subsequent raids.
Investigators decided not to charge the owner of the monazite, Hiroshi Ikeda, due to a lack of laws covering storage of the radioactive material.
Formerly the operator of a trading company, Ikeda sold the monazite, which was isolated from a mineral substance he obtained in Thailand decades ago, to create hot water for spas.