Matt Scott replaces injured Alex Dunbar at centre for the match being played at Toyota Stadium in Aichi Prefecture, while Stuart McInally comes in at hooker for the injured Ross Ford.
Harlequins-bound Ruaridh Jackson will start at flyhalf and Jonny Gray returns to the second row to partner brother Richie at lock.
"We want to get a decent set piece and do things simply," Cotter told reporters.
"They play with confidence and play in a certain way that is effective. They will be a fast, mobile team and it will be hard to get the ball off them."
The second test is in Tokyo on June 25.
Team: 15-Stuart Hogg, 14-Tommy Seymour, 13-Duncan Taylor, 12-Matt Scott, 11-Damien Hoyland, 10-Ruaridh Jackson, 9-Greig Laidlaw (captain), 8-Ryan Wilson, 7-John Hardie, 6-John Barclay, 5-Jonny Gray, 4-Richie Gray, 3-Willem Nel, 2-Stuart McInally, 1-Alasdair Dickinson
Replacements: 16-Fraser Brown, 17-Rory Sutherland, 18-Moray Low, 19-Tim Swinson, 20-David Denton, 21-Henry Pyrgos, 22-Peter Horne, 23-Sean Maitland
(Reporting by Nivedita Shankar in Bengaluru; Editing by John O'Brien)
