Nakasuga has previously made five MotoGP appearances, including a shock second place in the damp 2012 Valencia race.
The factory test rider and All Japan Road Race Championship star also joined Bradley Smith and Pol Espargaro in Yamaha's victorious Suzuka 8 Hour team earlier this season (pictured).
"Of course, I have my development duties for this year's Grand Prix of Japan, but being able to enter with special livery commemorating Yamaha's 60th anniversary has me even more motivated than usual," he said.
"I'll do my best to show Yamaha's strengths and how fast the M1 is together with Rossi and Lorenzo on the world stage, and I hope that I can make it a race to remember for Yamaha in its 60th year.
"Also, with the full factory entry, the debut of the new R1, and the goal of becoming a four-time consecutive JSB1000 class champio n, I started this season with more pressure than I've ever felt before. But in both my main arena of the All Japan Championship and the Suzuka 8 Hours, we've performed very well.
"I want to keep this momentum with me going into the Japan GP so I can leave some satisfactory results, and then take them with me to boost my JSB1000 season. I hope everybody will come to cheer us on at the race!"
