Koya director John Devitt said although it would be preferable for the Frith Street restaurant, which opened in April 2010, to remain open, it would not be the same without Yamasaki.
"While we would like Koya to stay open indefinitely as an extension of Junya's vision, we feel it will be a derivative that would not be fair to our customers," he said in a statement. "Koya has been a terrific journey for us all and we do not want that to be diminished.
"I personally would like to thank Junya for everything he has put in to Koya and his continued dedication driving Koya forward and especially the treat that was The BackBench over the last 12 months. Junya is a special talent, I wish him the best for the future and I hope to see Junya return to London soon."
Koya's neighbouring noodle-based restaurant Koya Bar, at 50 Frith Street, will remain open. Devitt said the company would continue to develop the concept with plans to open a second Koya Bar in the next few months.
Koya, at 49 Frith Street, will close on 31 May.