Meantime, an unheralded B-29 operation—originally unwanted—was setting some major marks of its own. The 313th Bomb Wing, operating out of Tinian's North Field, was mining Japanese waters. The sea lanes supplying the islands had been blocked by naval actions and the flow of commerce to Japan had been severely curtailed. Only one significant water route remained open, and it approached the Inland Sea through the Shimonoseki Strait at its eastern end. It was a narrow channel, eminently suitable for mining. The Navy had been after Arnold for months to divert some of his air strength for that job, and he finally acquiesced.

Missions were flown at relatively low levels, using APQ-13 radar and LORAN (long-range aerial navigation) for finding the target area and dropping the mines. The first attack was flown the night of 27 March 1945, by 92 B-29s; on 30 March, another force of 85 bombers sowed a second batch of mines and sealed the strait and its approaches. The only Japanese counter was mine-sweeping, a hazardous task in the presence of acoustic and magnetic mines. No Japanese warship larger than a small destroyer got out of the strait after those first two weeks. Destroyers tried to clear the waters when they were ordered to Okinawa to try to assist in the defense against the American amphibious assault, but four of them were blown out of the water by the mines. By the end of April, the toll was 18 ships either on the bottom or permanently disabled in the strait.

LeMay ordered that one bomb group concentrate on the mining missions unless needed elsewhere for a top priority strike against a ground target. The 505th BG (H) became the specialist unit; they flew a flurry of 14 missions in less than a month, mining 10 major shipping lanes in the Sea of Japan and the Inland Sea.

The record mining mission was flown by a 6th BG B-29 from Tinian to the Korean port of Etashin, 2,362 miles (3,800 km) distant. It dropped its mines in the harbor approaches and flew home. It was airborne for 19 hours 40 minutes, and had covered 4,724 miles (7,600 km) nonstop.

It was a very productive use of the bombers. The 12,000 mines they sowed destroyed more than 10 per cent of all the merchant shipping that Japan lost from late March 1945 until the end of the war.

Lesser results came from the precision bombing by radar of Japanese oil storage and refining facilities. The 315th BW (H) arrived at Northwest Field, Guam, in May and June 1945, equipped with late-model B-29Bs. They were specialized planes that had no top or belly turrets; only the tail gunner's position remained for defense. Their bellies were painted a glossy black to defeat the searchlights. And just below the belly was mounted what looked like a small wing, the radar antenna of the APQ-7 'Eagle' system, a new and more accurate blind-bombing radar.

The 315th flew 15 missions using the 'Eagle' system. They were able to carry larger-than-standard bomb loads, because of the weight saved by the elimination of turrets and fire-control system. On later strikes, the bomb loads were close to 10 tons.

Japan was too far gone for these missions to have had any but secondary effects. The oil came in from overseas, primarily, and blockades and mining had dried up the supply that might otherwise have been stored and refined in the targets that the 315th struck.