The Edinburgh hooker has been replaced in the squad by the uncapped Adam McBurney.
It’s tough luck on Cherry who sustained the injury in Sunday’s Rainbow Cup match against Scarlets in Wales.
He made his international debut this season at the age of 30 when he came on as a substitute in the historic win over England at Twickenham. He continued to play a key role for Scotland in the Six Nations, including scoring two tries on his first international start, in the victory against Italy at Murrayfield in March.
His absence from the summer programme opens the door for McBurney, the Ulster hooker who will join Edinburgh next month.
Ballymena-born McBurney represented Ireland up to under-20s level, but qualifies for Scotland through a grandmother from Cadder, Lanarkshire.
Interim head coach Mike Blair will lead a largely inexperienced national squad over the summer. They will play an A international against England in Leicester on June 27 before heading to Eastern Europe for Test matches against Romania on July 10 and Georgia on July 17.
The other hookers in the 37-man squad are Ewan Ashman, the uncapped Sale Sharks forward, and Glasgow Warriors pair George Turner and Grant Stewart.
Blair, who is in charge while Gregor Townsend is away on British and Irish Lions duty, is expected to trim the squad after the game against England A.
Scotland lost back-row forward Matt Fagerson to injury on Monday and added Northampton Saints centre Rory Hutchinson to the squad.