The big-hitting batsman and fast bowler, who only qualified for the Scots when ICC officials changed eligibility rules last year, will be available to lead Scotland's World T20 qualifying bid later this year.
Carter's absence comes on top of an injury which is likely to rob the Scots of their captain, Kyle Coetzer, when the Australians pitch up at the Grange, Edinburgh, on Tuesday.
Pete Steindl, the Saltires coach, said: "It's disappointing to lose a player of Neil's ability and experience. He has recently taken a coaching job in South Africa and that has to be his priority at the moment. However, it looks as if he could be available for the T20 qualifiers later in the year."
Preston Mommsen will captain the side if Coetzer does not make it. Steindl added: "We'll continue to monitor Kyle and the medical people will have the final say but it's not looking too hopeful."
Coetzer's Northamptonshire team-mate, wicketkeeper David Murphy, is preferred to Matty Coss and Craig Wallace who have vied for the gloves for most of the season. Three more members of Scotland's county contingent, Matt Machan, Rob Taylor and Iain Wardlaw, are also included. Hamish Gardiner could earn his first full cap against the country of his birth while Safyaan Sharif returns for the first time this season after a back injury.