A very good reference on demobilization
http://www.history.army.mil/books/wwii/MacArthur%20Reports/MacArthur%20V1%20Sup/ch5.htm
In the over-all picture, enormous military risks were involved in landing initially with “token” United States forces. The Japanese mainland was still potentially a colossal armed camp, and there was an obvious military gamble in landing with only two and a half divisions, then confronted by fifty-nine Japanese divisions, thirty-six brigades, and forty-five-odd regiments plus naval and air forces
One of the most interesting features of the disarmament program was the disclosure of the precarious condition of the Japanese defending forces in the home islands. After Allied victories of Iwo Jima, Okinawa, and the Philippines and the establishment of Allied naval blockade of China, only the troops in Japan were supplied by the homeland. On 31 August 1945 the Japanese reported on hand 1,369,063 rifles and light machine guns with limited ammunition of only 230 rounds per weapon. Records later indicated that actually some 2,468,665 rifles and carbines were received by the Occupation forces and later disposed of. The Japanese reported more artillery ammunition than small arms ammunition. Ammunition for the grenade launcher, often known as the “knee mortar,” was also more plentiful; some 51,000,000 rounds were reported, or an average of 1,794 rounds for each weapon.
Ammunition and weapons, particularly small arms, could have been hidden easily by rebellious individuals or groups, only to be brought out at some later time in revolt against the Occupation forces. Apparently there were more than a few abortive attempts in that direction, for although the Japanese military commanders appeared to be acting for the most part in good faith in surrendering their arms and equipment, every month of the Occupation disclosed new caches of military supplies. Though the caches usually were not heavily stocked, their very existence was enough to indicate that the chain of Japanese responsibility had broken down somewhere. Thorough reconnaissance and inspection by the Occupation forces brought to light many situations which were resolved before they could become serious problems.44 For example, a check on the police stations in Aomori, Hirosaki, and Sambongi (all towns in Aomori Prefecture) produced some 1,880 rifles, 1,881 bayonets, 18 light machine guns, 505,260 rounds of rifle and machine gun ammunition, 46,980 rounds of blank ammunition, one case of TNT, and 150 military swords. Daily G-2 and CIC reports revealed many instances of smaller caches, sometimes in school compounds. Officials and teachers, when questioned, usually pleaded ignorance, and very often investigation did show that faulty dissemination of instructions had been the root of the trouble.45
All Japanese ammunition, bulk explosives, and other loaded equipment (ordnance, chemical ammunition, and engineer explosives) were destroyed without delay, with the exception of items desired for technical intelligence purposes. The principal method utilized was dumping into the sea at a depth in excess of 300 feet (later 600 feet).
Imagine the military suggesting, much less doing, such a thing today. OTOH, I can't think of any lasting environmental damage that occurred because of the dumping.