There were two categories of economic costs faced by Japan during this time. One was the cost of the war materiel that was needed to fight. The other was the cost in damages to Japanese people and industry.
The war, of course, cost a lot of money to fight. The Japanese had to pay for all the ships and airplanes and bombs and bullets that were used. However, an even larger cost might have been the cost in lost property and lives. The bombing of Japan devastated cities. US submarines sank ships carrying tons of goods. Most importantly, something like 3 million Japanese military personnel and civilians were killed in the war. These losses of property and lives were major costs because they reduced Japan's economic potential once the war was over.