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Quick look showed that not all banks in Japan handle exchange from Czech Koruna to Japanese Yen.

If you are arriving at Narita Airport, there are several different banks with currency exchange desk but looks like only two of them handle Czech Koruna; GPA Travel Support and Keio Bank.

Today’s rate at GPA Travel Support for exchanging from Czech Koruna to Japanese Yen is 1 Koruna to 4.13 Yen, where official exchange rate is 1 koruna to 4.916 Yen. You will be losing 16% value exchanging at Narita Airport. This exchange rate includes service fees.

It is possible that a bank has further restriction such as denomination accepted and minimum and maximum on cash exchange. I am guessing that Czech Koruna is not particularly commonly handled currency in Japan, from the fact that not all currency exchange desk at Narita Airport handle Czech Koruna, and not all banks in Japan handle exchange between Czech Koruna and Japanes Yen.

P.S.
You are also looking to exchange Hungarian Forint. Hungarian Forint is similar situation as Czech Koruna, not all Japanese banks handle cash exchange between Hungarian Forint and Japanese Yen.