I applied for a tourist visa to Japan and paid a deposit of 50 thousand. I don't want to go now, and the deposit can be refunded.

The deposit is collected by the travel agency and has nothing to do with the embassy. The embassy won't charge you anything except the visa fee. If you sign a travel contract, you have to abide by it. Generally speaking, the contract will stipulate how many days in advance to cancel the corresponding losses. But this refers to your travel expenses, not the deposit. The deposit will definitely be refunded to you in full. If you cancel your trip a few days in advance, the tour fee you paid will be deducted.