The decision by Gordon Brown to allow the Church of England to choose its own bishops for the first time since Henry VIII was broadly welcomed by Church leaders yesterday.
But the reform - one of the biggest changes in the relationship between Church and state since the Tudor king fell out with the Pope - will reopen the fraught issue of disestablishment.
It will also dismay many Anglicans that such a major reform could have been announced with so little consultation or public debate.
Mr Brown was at pains yesterday to minimise the fuss by overtly supporting the Church's established status, a constitutional arrangement supported by most churchgoers.
His announcement is nevertheless bound to refuel the demands of a vociferous minority for all ties to be cut between Church and state, including the right of bishops to sit in the Lords.
The row will surface next week when the General Synod meets in York as a debate on senior ecclesiastical appointments is already on the agenda.
The Archbishop of York, Dr John Sentamu, who is heading the Church while his counterpart at Canterbury is on leave, played down the impact of the reforms yesterday.
He pointed out in a statement that the new arrangements for choosing bishops had originally been proposed by the Church itself 33 years ago.
In those days, the Crown had the sole right to appoint archbishops or bishops when vacancies arose without reference to the Church.
But a report endorsed by the Synod in 1974 recommended changing the system to allow the Church to forward the name of just one candidate to the Prime Minister.
This was too radical a step for the then holder of the post, James Callaghan.
He devised the compromise under which the Crown Appointments (now Nominations) Commission forwards two names, allowing the Prime Minister to choose one to pass to the Queen or, in rare cases, ask for more names.
Yesterday, however, Mr Brown effectively introduced the Church's original proposal by surrendering his right to select between different candidates.
He also made clear that he would do the same for other senior ecclesiastical appointments still made by the Crown, including a number of cathedral deans and canons.
But the Queen will retain her role in appointing deans to the so-called "royal peculiars", the handful of churches and chapels, including Westminster Abbey, which have an historic royal connection.
Welcoming the proposals, Dr Sentamu said in his statement that Mr Brown had consulted both him and the Archbishop of Canterbury, Dr Rowan Williams, about his intentions.
He said he was "grateful" for the Prime Minister's backing of the continuing role of the Queen and the "establishment by law of the Church of England."
"The challenge we face as the Church of England is to use the sacred trust, enshrined in law, for the common good of all the people of England," he said.
"Our vocation is to love God and to love our neighbours as ourselves: doing to others that which we would wish to be done to us.
"Our presence in every part of England must be used for bridging, bonding, partnership and friendship for all."
But some clerics said that the removal of Downing Street from the process of choosing bishops and deans could further concentrate power in the hands of a few senior prelates.
Canon David Holding, a Synod member, said: "This goes to the heart of the Church/state relationship. It has huge implications.
"It will threaten the diversity of senior appointments, and could well lead to the old boy network running riot."
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