Vanier said he did not believe he could be "held responsible". Radar Films declined to comment.
Olivier Gourbinot of France Nature Environnement said: "There are only 4500 pairs of flamingos in France and 500 were disturbed. Each pair lays only one egg and an estimated 500 eggs were abandoned, so at least 11 per cent of the eggs from the country's only flamingo colony were destroyed."
He said researchers in the area saw one of two planes used for the film fly over the flamingos at low altitude.
Vanier said: "I was outraged. The pilot had been given a flight plan that specifically indicated the areas to avoid."
Vanier, 56, best known for films such as Wolf and The Last Trapper, is making a film called Give Me Wings about a scientist's passion for wild geese.
On Monday he said he had halted aerial filming in France after the flamingos were disturbed and is completing the project in Norway.
Vanier, who is also a writer and adventurer, said he wishes to "repair whatever can be repaired" and has proposed to French environmental groups that he "sponsor" the flamingos and become a "spokesman for the problems suffered by migratory birds".
Simon Popy, head of France Nature Environnement, said the group "would prefer to let a court settle this matter".
He said flamingos "are extremely sensitive when hatching their eggs. They abandon them easily and once abandoned, they don't return".
Flamingos are migratory and the numbers present in France each year have fallen by more than 75 per cent from about 20,000 a few decades ago, Popy said.
The decline is believed to have been caused in part by a reduction in salt production, resulting in a loss of wetlands habitat for the birds because fewer areas are being deliberately flooded with seawater to make salt.
The flamingos are now concentrated on an artificial island, where they breed.
It is not the first time Vanier has been embroiled in controversy. In 2014, he was ordered by French authorities to remove dogs from his nature park in southern France because they were being held in unsafe conditions.
At the time, the director said the dogs had never been maltreated and blamed the manager of the site for failing to comply with safety requirements.
Vanier said the film he is currently making deals with bird conservation, but Popy said it was "controversial" because it tells the story of a scientist "who attempts to make geese change their migration routes, an approach to nature that is questionable".