Minister for Community Safety and Legal Affairs, Roseanna Cunningham, said: "A Yes vote means that Scotland will have a written constitution and that means everyone can be assured that the constitution in place on Independence Day will uphold the rights and liberties of all, including freedom of religion and the protection of Catholic education."
Some members of the No campaign had expressed concerns that faith schools would be under threat if there was a yes vote in Thursday's referendum.
Scots will be asked to answer yes or no to the question, 'Should Scotland be an independent country?' when the polls open on September 18.
In May, Respect Party MP George Galloway said Catholics should be 'careful what they wish for' and said that as a Catholic he would have concerns about living in an independent Scotland led by the Scottish National Party (SNP).
He told the Sunday Herald: 'I recently floated, on Twitter, that Catholic schools would not survive more than a decade in an independent Scotland and I was deluged with people saying 'yes, quite right'.
'Now, you may be against Catholic schools, but Catholics currently have the right to send their kids to Catholic schools and that is a right which will undeniably be in danger in an independent Scotland.'
The official Better Together campaign has distanced itself from the claims.
Meanwhile, an advert has been placed in a Scottish newspaper by a number of Catholics who are urging others to vote yes.
Scotland's former chief medical officer, Sir Harry Burns, former Strathclyde regional council leader, Professor Duncan MacLaren, and various members of local clergy have all signed the open letter.
It said: 'We believe a Yes vote in this week's referendum makes possible a more socially just Scotland.'
The lead duo of Scottish band Deacon Blue have also signed the letter, which was organised by campaign group Christians for Independence.
However, a similar number of Christians has joined the Faith in the Union group, which is campaigning for a No vote. It is led by Labour peer Willie Haughey and former home secretary John Reid.
Lord Reid said: 'I am a proud Scot and want the best for my country. That's why I will be voting No to separation in September. A No vote is a vote to protect the best interests of Scotland and its people.'