Aileen Campbell, minister for children and young people, has explained that her personal views differ from the stance taken by the Scottish Government.
"The Scottish Government's position is that after a yes vote next year the Queen would remain the head of state but like many people in Scotland I believe the sovereignty of people is a very important thing so it would be up to people to decide whether or not that would remain the case thereafter," she said on the BBC Three programme Free Speech.
Alex Salmond has previously stated that the result of the referendum next year will not change the role of the monarchy in Scotland.
Last month the chairman of the Yes Scotland advisory board, Dennis Canavan declared that the newest member of the Royal Family and third in line to the UK throne should never be king of Scotland.
It's a view shared by others in the pro-independence campaign including the Scottish Green and Scottish Socialist parties but conflict with those of the Scottish National Party and Scottish Government who wish to see the retention of the monarchy.
The First Minister has not said there would be a referendum on the Queen being retained as head of state, yet Ms Campbell has suggested otherwise.
Speaking on the TV show: "I think it's up to folk, folk like yourselves here in the audience who will have a say on how the country is shaped as we move forward and I think that's a really exciting thing.
"The birth of a child is always a happy event and I'm sure everyone wishes Prince George all the very best but for the country to move forward, a yes vote next year will allow us and enable us to take the decisions about what that country would look like, how it would feel and that includes about deciding who is the future head of state."
In response to Ms Campbell's comment, Scottish Conservative deputy leader Jackson Carlaw said: "It is increasingly clear that many leading SNP MSPs and MPs are doing nothing other than paying lip-service to the First Minister's assertions that the Queen would remain the head of state of an independent Scotland.
"They clearly want a referendum and a republic and the only thing stopping them from saying so is the knowledge that the Scottish people are comfortable with and support the monarchy and that by being honest about their intentions support for independence would slump even further.
"Scotland is facing its biggest decision for 300 years and the public deserve absolute clarity on what a separate Scotland would look like rather than the First Minister and his party contradicting each other over such a crucial issue."
Ms Campbell said: "As usual, the Tories are making mischief. All I was pointing out is that different parties can propose different policies in each election after independence, and that - just like in the UK - our constitutional monarchy rests on the consent of the people.
"The Scottish Government and SNP position, which I support, is clear - an independent Scotland will retain the Queen as head of state. The Queen is already monarch of 16 independent states in the Commonwealth, and a Yes vote next year will mean an independent Scotland will take its place as the seventeenth."