David McLetchie, the party's leader, wrote to Donald Dewar, the First Minister, to protest at proposed return of St Mary's primary in Dunblane and Dornoch Academy to local authority control, in contrast to Jordanhill School in Glasgow which will continue to be independently managed.
Brian Monteith, the Tories' education spokesman, had sought to profit last week from the fact that Sam Galbraith, the Children and Education Minister, sends his children to Jordanhill.
The issue is linked to the Tories' policy of removing education from council control.
In his letter Mr McLetchie says the decision places Mr Galbraith in an invidious and untenable position as a Jordanhill parent. "He is exposed as another in the long line of Labour hypocrites who advocate one thing for other people's children while doing the complete opposite for their own."
Mr Galbraith declined to comment this week. Mr Dewar's office had not received Mr McLetchie's letter on Monday.
The Tory leader told the First Minister: "I can only assume that Sam Galbraith's decision to send his children to Jordanhill and his decision to allow it to keep its freedom is based on the fact that it is an excellent school, which has benefited from its existing status.
"If this is so, then why deprive other schools of the ability to develop free of local authority control and other parents of the opportunity of sending their children to such schools?
"Far from higher standards in Scottish education, your Government is now synonymous with double standards."
Jordanhill is funded directly by the Scottish Executive Office, a decision taken by the Conservative government in the mid-1980s when the two alternatives of becoming fee paying and "opting in" to the former Strathclyde Region were rejected. It had previously been a demonstration school for the teacher training college.
The school's exam results have consistently outshone those of local authority schools, with 62 per cent of fourth-year pupils gaining five or more Standard grades at Credit level last year compared with an average of 18 per cent for Glasgow secondary schools.
But, like all such results, Jordanhill's score is subject to fluctuation: 76 per cent of the fourth year gained five-plus Standard grades at Credit level in 1997.