The deficit is the difference between the existing allocation spent in South Ayrshire by Kyle and Carrick DC and Strathclyde RC - a sum of around £111,678,000 - against a Scottish Office assessed figure for the new council of £110,901,000.
Chief executive of South Ayrshire George Thorley said that unless the deficit is addressed by the Scottish Office, there would be an increase in band D council tax of £19.14.
It has also been revealed at a meeting between the Scottish Office and COSLA that the new City of Glasgow UA would not receive additional funding and the Scottish Office indicated that a 'local solution' would have to be found.
This would result in band D council taxpayers in South Ayrshire seeing an increase of £99 per annum 'for no new service, no provision for funding wage/salary awards of even contingency funding to cope with new legislation'.
Leader of the council Ian Welsh said:
'We are calling on the government to take action quickly as it's grossly unfair for the people of South Ayrshire to be penalised as a direct result of local government reorganisation. If nothing is done, we will all end up paying much more for the same, or perhaps less, services than we have now.'
Deputy leader John Baillie said:
'This situation exposes the myth that reorganisation would save council taxpayers money. Before the new council has even begun to operate, the Scottish Office is trying to saddle us with an enormous financial burden.'