"This morning, we confirm, as the bond administrator, that we received 20 billion yen in principal and interest," a Mizuho spokesman said. "Now we have started the process of returning the proceeds to investors."
First issued by the Asian Development Bank in 1970, samurai bonds offer a way to tap Japanese investors by issuing debt in the country's own currency.
In 2001, Argentina defaulted on a series of yen-denominated bonds while US brokerage Lehman Brothers failed to make good on its samurai bonds in 2008.
Greece "wanted to secure access to capital markets by meeting its obligations to private investors", said Sayuri Ito, senior researcher at NLI Research Institute in Tokyo.
But Ito warned that any new yen bonds issued by Greece would only be for investors who have "a very high risk tolerance".
The small refund comes after Athens missed the second debt payment to the International Monetary Fund in two weeks on Monday, despite having reached agreement with official creditors on a new bailout programme earlier in the day.
Greece was supposed to remit about 456 million euros ($500 million) to the crisis lender, although it had not been expected to make the payment after missing a 1.5-billion-euro debt payment to the Fund on June 30.
Greece's arrears to the IMF now total about 2.0 billion euros.