In a series of blog posts, the Most Rev David Chillingworth, the Bishop of St Andrews, Dunkeld and Dunblane wrote: "The Church of Scotland and the Church of England seem to have decided that their commonality as National Churches justifies them in setting aside other ecumenical relationships and etiquette."
News that the CofE and CofS had reached an agreement to work more closely together was set out in a 15 page report published on Christmas Eve.
David Chillingworth is calling for the publication of the full document to be delayed to allow time for consultation to take place.
One of his concerns is that the Church of England will begin to have a say on spiritual matters pertaining to Scotland.
"The Church of England is not a Scottish Church nor does it have any jurisdiction in Scotland. The Anglican way is to recognise the territorial integrity of each province - they are autonomous but inter-dependent."
He also believes the agreement introduces confusion on a number of matters, including worshippers attending other denominations and swapping preachers.
He says the Columba Declaration "...suggests that the Church of England will respond warmly to the idea that its members will worship in Church of Scotland churches when they visit Scotland. Yet the Church of England's Anglican Communion partner in Scotland is the Scottish Episcopal Church.
"The second - and far more serious - provision is that the partners will 'enable ordained ministers from one of our churches to exercise ministry in the other church'...Yet the Church of England and the Scottish Episcopal Church are partner members of the Anglican Communion. The Anglican Communion in Scotland is expressed in the life of the Scottish Episcopal Church."
The Most Rev David Chillingworth says that this, and the rest of the Columba Declaration, has caused "deep hurt" to the Scottish Episcopal Church, which has 35,000 members.
Responding to the Bishop's comments, the Church of Scotland denied that the Scottish Episcopal Church had been side-lined.
"The joint study group report and the Columba Declaration are the outcome of ecumenical work that has been under way since 2010," a spokesman said.
"The Scottish Episcopal Church was a full partner in the joint study group until it chose to withdraw from active participation in 2013."