Banchory Academy Parent Council is concerned that in future pupils will only be able to study five subjects in S4, compared with the current eight.
They say this will reduce children's future options and harm their chances of getting into university.
Louise Christophersen, the Banchory parent council chair, said two families were moving their children to an independent school, Robert Gordon's College in Aberdeen, because of the issue.
Eileen Prior, executive director of the Scottish Parent Teacher Council, said they were likely to be just the first of many.
And Scotland's main union for secondary teachers, the Scottish Secondary Teachers' Association (SSTA), said they had expressed concerns about limiting pupil choices for the last three years.
The Aberdeenshire parents are concerned that because new exams are expected to be taken only in S4 - rather than S3 and S4 as Standard Grades are currently - there will only be enough time to study five subjects.
Christophersen told Scotland on Sunday: "Many parents in Scotland are still unaware of the proposed changes or are confused by the information they have had access to.
"In fact, on the SQA website there is a sample timetable for Charleston Academy showing eight subjects. But this can only be done if options are started from S3 as at present.
"If options are started from S4, as proposed under CfE, the number of hours required to cover each course will only allow five subjects to be studied."
A Scottish Government spokesman said: "Curriculum for Excellence is providing pupils across the country with a rich and flexible learning experience and young people will be able to study up to eight subjects from S4.
"The SQA is liaising with parents and parent councils to help explain developments, although the precise number and choice of qualifications provided will be a decision for schools to take in consultation with learners and parents."