The 22-year-old, who has appeared 11 times for his country, scored 13 goals in 33 matches for FC Tokyo in his first J-League campaign to equal a newcomer’s record.
"We've been watching Muto for a long time now because we're certain he suits Mainz 05 and our style of play," Coach Martin Schmidt told the club's official website.
"He's quick, agile, and a very technical forward for the flanks, who will bring further quality in this position."
The highly regarded Muto won his first cap for Japan last year when he appeared against Uruguay on September 5. He duly scored his first international goal against Venezuela just four days later.
Muto will join forces at Mainz with compatriot Shinji Okazaki.