Deer stalking experts have advised the cull should go ahead after six deer died in the past year from disease following inbreeding.
However, deer campaigners are calling for the deer to be captured and released elsewhere.
Darting roe deer so they can be moved is said to have a 50% fatality rate.
The old Diageo bottling plant site, where the deer are trapped, was fenced off 10 years ago.
A Diageo spokesman said: “Diageo has been working closely with deer welfare advisers at the Deer Commission for Scotland, the British Deer Society and the Scottish Deer Centre and with animal welfare officers at the SSPCA in a determined effort to address the animal welfare issues of a small herd of roe deer that has taken up residence at our Leven packaging site.”
“There have been deer on site for around 10 years, but recently there has been concern about the increasing numbers and health of the deer.”
“However, the advice from the deer experts is that it would be irresponsible to relocate the deer and in the best interests of animal welfare all the deer should be culled.”
Alastair Macgugan, stakeholder manager for the Deer Commission for Scotland (DCS), said: “This is a very difficult situation but we feel that Diageo has made the best decision, given that it isn’t possible to relocate the deer and that the roe would not survive well – and would suffer in the long term – if left on the plant site.”
Jamie Hammond, DCS deer officer, said: “They have liver fluke, which is exacerbated when deer are in a high density and on poor quality land. The deer are also hefted to that site, which means they see the site as their home.”
John Robins, of Animal Concern Advice Line, which has been campaigning against the cull, said: “Believe it or not some groups have suggested that the deer should be killed for their own welfare. Absolute nonsense. The animals can easily be released back into the wild or transported to one of the two new homes offered for them in the local area. Those who have suggested killing them are from what is known as the Harold Shipman wing of the conservation and animal welfare movement.