When renting an apartment yourself, you must pay various fees, such as a deposit (shiki-kin) and key money (rei-kin). The expense differs according to region and apartment, but in general, as a rough estimate, you should think in terms of needing the equivalent of six or seven months' rent in the first month.
Many people go to real estate agencies to look for private accommodation. Since it is difficult for foreigners to follow the special commercial customs of Japan, may be strongly advise you to go to an agent with a Japanese person, preferably your guarantor.
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