However, Edinburgh City Council issued a listed building enforcement notice to owner, Anders Povlsen, and tenant Mike Ashley requiring for the iconic signs to be reinstated.
Mr Ashley has three months to comply until the notice comes into effect on May 14.
The lettering to be reinstalled is on the Princes Street and South St David Street frontages, according to the council.
Neil Gardiner, the Council's planning convener, said: "We can confirm that a listed building enforcement notice has been sent to the owner and the tenant of the building.
"It requires the lettering to be reinstated in its original positions on the Jenners building."
As well as the iconic gold lettering, passers-by have also spotted ‘Jenners’ signs being scraped off doors and archways of the building.
However, the council commented that the removal of low level signage on the building does not raise any planning issues.
Terry Levinthal, director of the Cockburn Association, said Edinburgh’s civic trust welcomed the calls for reinstatement from the council.
He said: “The association welcomes that step taken by the city council which is quite a positive one.
“We are very pleased they have taken this action and we look forward to the next chapter.
“The unique element of the Jenners store which isn’t generally appreciated is that it is the oldest department store that has continuously traded from the same site.
“As part of its history, things have been added including signs which have been fixed to the buildings and therefore – in terms of the technical application of the statute on listed buildings – they are deemed to be a physical part of the structure.
“Jenners is one of those iconic bench marks of the city and even though Jenners has ceased training as a building it will still be known as Jenners.
“A hundred years from now we will still be referring to that building as Jenners.”
Asked whether damage has already be done, Mr Levinthal said that part of the council’s process will include repairing the condition of the signage.
He said: “There will be discussions of what exactly that is going forward but it is a fundamental part of that action and any action of damage towards the signs will need to be remedied as part of the reinstatement.”
A spokesman for Povlsen said the signs were removed without his authorisation last week.
According to Edinburgh Rope Access who were tasked with taking the signage down, it is now being stored on the sixth floor of the department store.
Earlier this year, Mike Ashley's Frasers Group, which includes Sports Direct, announced that it was closing the landmark store after 183 years over failing to agree a “fair” rental agreement with landlord, Povlsen.
It was understood, however, that the sign would remain.
Frasers Group were contacted for comment.