The 2,000-strong common tern colony on a man-made island in Imperial Dock was abandoned this month.
Naturalists claim that increased shipping activity has scared the birds away, after dead terns and abandoned eggs were found at the site last month.
TV wildlife presenter Chris Packham has branded it a “tragedy in contemporary conservation”.
Common terns are at risk in the UK, rated “amber” by the Birds of Conservation Concern review. The Leith tern colony was the third largest in Britain and Ireland.
Forth Ports has denied claims that increased shipping activity has caused the destruction of the site and claims local tug crews “thought they saw a stoat or similar”.
The finding was rejected by the Lothian Ringing Group – local naturalists who have followed activity of the tern colony closely for 30 years.
John Davies, a member of the group said, “One mink attack doesn’t cause colony abandonment. Mink don’t leave dead birds lying about, they cache them in a hidden store and the same with eggs.”
Naturalists believe the impact of vessels loading materials from an adjacent pipe-coating plant has been disastrous for the birds.
Packham, the Springwatch presenter, has criticised Scottish Natural Heritage (SNH), accusing them of negligence. “SNH should have been far more diligent about the potential harm that could come to this colony and at this time of year it is illegal to disturb these birds,” he said.
A spokesperson from Forth Ports said: “A crew member on one of our tug boats discovered that the colony of terns appeared to have been attacked by a natural predator, resulting in the death of a number of the terns.”
A SNH spokesperson said, “Our staff confirmed the colony had been abandoned and there were clear signs that a predator such as a mink had attacked the birds and their eggs, which was confirmed by our marine ornithologists.
“Over the past 20 years the colony has grown to become the largest in Scotland and there has not been an incident of this scale before.”
A Scottish Government spokesperson said: “The area is classified as a Special Protection Area.
“Competent authorities are required to take appropriate steps to avoid significant deterioration of habitats or disturbance of the species.”