Rev Mark Binney, vicar of St Andrew’s Church, Hampton, Worcs, said he had been told he needed planning permission if he wanted to fly a flag “advertising Christianity” in future.
The flag was put up outside the church in the week preceding Easter Sunday displaying the words ‘This is Holy Week’ and an image of Jesus on the cross.
Mr Binney said the warning was “appalling”, and he felt it was part of a gradual erosion of Christianity in Britain.
Wychavon council said it investigated a complaint from a member of the public and decided no consent was required.
A spokesman said flags other than national flags, county flags, or flags for patron saints, required advertisement consent if they were flown from a vertical freestanding flagpole.
He said the council would consider allowing the flag to be flown for a week in future if it was approached by the church.