According to the Daily Post the council told Rev Bob Marshall (above) that the sign, which he's kept outside his Ebenezer Chapel in Buckley for years, requires permission because of its size and positioning on the street.
Rev Marshall has become well-known for his thought-provoking and often humorous messages on the sign.
It currently reads: "too many people have a strong will and a weak will not". A previous one read: "honk if you love Jesus; text while driving if you want to meet him."
The Baptist minister told the paper: "We are a church, not a business and these are not adverts and it is on our property.
"I don't understand why the council has asked me to do this now, I have been doing it for a few years.
"It just seems a bit petty and it's like as though they are trying to show who's in charge."
The council stressed their order for Rev Marshall to obtain permission for the sign is nothing to do with the spiritual messages on them, but solely because of where it is and how big it is. Businesses which have street signs of similar sizes also have to obtain permission.
Andrew Farrow, Chief Officer Planning and Environment, said: "Following receipt of complaints in relation to the size and positioning of the sign, not the specific messages displayed on the sign, we have advised Reverend Marshall of the need for planning permission.
"We would welcome further discussions with Reverend Marshall and we will be contacting him with a view to resolving the situation."