Bristo Baptist, on the Capital’s Queensferry Road, had previously applied for permission to hoist the aluminium cross adorned with LED lights above its main entrance where it would be visible through a window.

However, the church was shocked to have the plan turned down by City of Edinburgh Council even though the authority had received no objections to it.

The church was told that the cross would have a “detrimental impact” on the area.

The church disputed this and appealed to the Scottish Government in a bid to have the decision reversed.

Now, government reporter Jo-Anne Garrick has scrapped the council decision and given the cross the green light.

Reverend Garry Ketchen, minister of the church, which has nevertheless scrapped a second plan for an outside sign, said: “We were perplexed when we discovered the decision.

“We could understand some issues with the signage but not with the cross.

“The cross would be within our own building and the window is about three metres long and isn’t completely see-through either.

“There were no objections to our knowledge and we are now looking for a way of putting across our position and seeking some clarification on what exactly is the problem.

“It was being put in as our way of marking the church’s 250th anniversary.”

In a letter to government planning chiefs, the church said: “The cross was proposed by the congregation to mark the 250th anniversary of Bristo Baptist Church.

“The original application included an illuminated church name sign which is not being appealed.

“Although the cross, when illuminated, will be visible from outside through the north facing window it will be located inside the church so there will be no alteration to the outside of the building.

“The cross when illuminated will be a statement to the neighbourhood that the church is open and active.”

Council planners wrote to the church in June telling them the ‘proposed signage is inappropriate and would have a detrimental impact on visual amenity.’

Government reporter Ms Garrick said: “I note that the appellant wishes the cross to be illuminated so that those who utilise the facilities provided at the church can see when it is open and active.

“However, given the size and position of the proposed cross, particularly as a result of its location inside the church behind semi-opaque bevelled glass, I am satisfied that it would not appear excessively prominent.

“I conclude that it will preserve the character and appearance of the conservation area, will not detract from the special interest of the listed building and will not be harmful to amenity.”

A council spokeswoman said: “We note the decision taken by the Reporter regarding this appeal. However, it is important to note that the sign, which was the contentious of the two elements, was dropped and not taken to appeal.”