Mr Jones, whose store has become one of the most iconic on the busy strip since it opened more than 20 years ago, said he was concerned that the street was being divided.
His store, located on the eastern side of Beaufort Street, will be governed by the City of Perth.
But businesses on the opposite side of the road, north of Vincent Street, including The Flying Scotsman will be governed by the City of Stirling.
The City of Bayswater will control the road north of Walcott Street.
‘This section of Beaufort Street is going to be neglected as it will be shared by two councils with different agendas,’ Mr Jones said.
He said he was concerned there would be different rules on either side of the street regarding parking, rates, waste and speed limits.
Beaufort Street Network co-founder and Vincent councillor John Carey said splitting the main street between three councils would become a ‘bureaucratic nightmare’.
‘We are being told by the government that they want to make Perth vibrant and boost tourism and that is what the Beaufort Street Network is trying to do for the Beaufort Street town centre and yet the biggest hurdle will be bureaucracy and we are not going to have to deal with one but three,’ he said.
Stirling Mayor David Boothman said he was ‘devastated’ that the City would lose control of the northern section of Beaufort Street and questioned the boundary lines splitting the road between councils.
Vincent Mayor Alannah MacTiernan said it did not make sense to put a boundary through the main road.
Cr Carey said he was also concerned that the Beaufort Street Festival would lose vital council sponsorship.
But Cr Boothman said his council had a history of supporting the Beaufort Street Festival and local businesses in the area.
Local Government Minister Tony Simpson said councils could make requests to the Local Government Advisory Board for minor boundary changes.