The news is the latest in a long line of blows to workers in the South Lanarkshire town, which has seen jobs slashed across a range of industries.
Coca-Cola Enterprises is consulting with staff over the closure of its Regional Sales Office and expects the process to be completed by early next year.
The plans are part of a wider cost-cutting exercise across the UK which will see 240 jobs cut from Coca-Cola's nationwide workforce of 4600 people.
A spokesman for the firm said: "It is too early to provide exact details of the impact locally in Scotland as we have only just started consultations with our employee representative bodies.
"However, we expect these proposals could result in a reduction of approximately 50 roles out of a total workforce of 359 in Scotland at our four sites.
"We are proposing the closure of our Regional Sales Office in East Kilbride – but we will continue to use part of the site as a supply depot for our vending operations in Scotland.
"The changes are proposed to be introduced in the early part of 2013 and we will, of course, be looking to minimise redundancies as far as possible and will offer support to help colleagues through this process."
In total, Coca-Cola currently employs 181 people at Milton Road in East Kilbride. It opened the site in 1964.
Manufacturing and bottling divisions at the base will not be affected by the cuts.
East Kilbride MP Michael McCann has spoken of his dismay at the job losses.
He said: "It seems like a week doesn't pass by without more bad news.
"The announcement that Coca-Cola will close down their East Kilbride sales office will be a body blow to staff and their families.
"The company have confirmed that they will do everything they can to minimise redundancies and, of course with a strong manufacturing presence in the town, there is a genuine hope that this can be achieved.
"However, there is no veneer that I can apply that can make this anything other than bad news for the town.
"I will be keeping in close contact with the company to follow the process and of course I will support the workforce in any way that I can."
Earlier this month, cleaning product giant the Jeyes Group announced it was consulting over closing its East Kilbride plant and moving 100 jobs to England.
And in August Rolls Royce said it was shutting its East Kilbride factory and moving 600 jobs to a plant in Inchinnan, Renfrewshire.