Very Rev Charles Taylor made the comment in his final sermon as dean of the area's cathedral, amid rumours his resignation was forced due to money issues.
At one point it looked like Peterborough Cathedral staff weren't going to be paid over the summer however the Church Commissioners - which have £7bn in investments - provided a loan.
Very Revd Charles said actions were being taken to make the Cathedral more solvent.
The priest claimed the Church of England didn't necessarily view the cathedral and others like it favourably because of the independence they might exert financially or theologically.
According to the Church Times he said: "It certainly does not conform to the ecclesiology, if one can call it that, of those who would like to see power concentrated at the centre, in order to impose a bland, uniform theology, if one can call it that, which runs counter to the very essence of Anglican diversity.
"Where among the leaders of today are the colourful clerics and turbulent priests, the prickly prophets, the rebels and reformers?"
"It is surely of salutary significance that newly appointed deans and bishops these days are sent on an induction course — not as you might think, to hone their skills in theology, or liturgy, community outreach, or pastoral care, but to take a mini-MBA.
"The pattern of the Good Shepherd has been hijacked by the model of the Chief Executive Officer."
The Bishop of Peterborough Rt Rev Donald Allister has called Mr Taylor "a man of the highest integrity and probity".
