Passers-by reported seeing the lettering being taken down by workers yesterday.
Earlier this year, Jenners owner House of Fraser announced that it was closing the landmark store after 183 years after failing to agree a “fair” rental agreement with landlord, Danish retail clothing billionaire Anders Povlsen.
Despite the closure, however, it was believed that the store’s familiar signage would remain.
A spokesman for Povlsen last night said they were "very surprised" the signs had been removed. He said they would be contacting Mike Ashley's Frasers Group, which also includes Sports Direct, and owns the commercial rights to the Jenners trading name.
Anders Krogh Vogdrup – the director of Povlsen’s group AAA United – told the BBC last night: "We are very surprised seeing the signage being taken down. We are convinced that the signage is part of the listed building.
“We have not discussed any such step with Sports Direct, and certainly not given any authorisation to do so. We will look in to this matter, contacting Sports Direct.
“We can only once again emphasise that the Jenners building of Edinburgh is an institution and, despite the changing face of retail, it is our aspiration that there will continue to be a retail store for as long as we are its stewards.
“Our involvement in the Jenners building, is first and foremost about helping to preserve a unique historic building in Edinburgh. Already when we acquired the building, we knew that it came with a great deal of responsibility.
“Jenners is an iconic building in Edinburgh, and we take the responsibility very seriously.”
It is understood that City of Edinburgh Council is investigating whether the removal of the signs was a breach of planning rules due to “the historical significance of the building".
Councillor Neil Gardiner, the planning convener, said: “We'll take action if appropriate”.
The Jenners building has been a fixture on Princes Street for 183 years.
It was bought by Mr Povlsen in 2017 for a reported £53m.
Jenners started when a pair of drapers, Charles Kennington and Charles Jenner, were sacked from their jobs for going to the Musselburgh races rather than turn up for their shifts.
They bought the lease on a converted townhouse property on the corner of Princes Street and South St David Street to start their own drapers.
Trading started on May 1, 1838 under the name Kennington and Jenner.
The boutique corner shop was soon expanded to become the largest retail establishment in Scotland. In 1892, disaster struck when the store burned to the ground.
With substantial insurance funds and financial backing from the town council, Jenners’ rebirth was spectacular.
Architect William Hamilton Beattie was enlisted to create a true Edinburgh landmark. The store continued to thrive during the 1900s and expanded several times to take up further retail space along both Rose Street and Princes Street.
In 2005, despite changing their mission statement to “Confidently Independent” the year before, the company was sold to its rival House of Fraser for £46 million after being family run for 167 years.