The acid, which most likely came from anchovies and squid which formed part of the birds' natural diet, can sometimes cause brain damage.
In severe cases, it leads to them becoming confused, suffering seizures, and dying.
Sibel Bargu, who led the research, said domoic acid was found in 79 per cent of the plankton ingested by anchovies and squid.
Over a short period that would become sufficiently concentrated to cause fatal injuries to predators who ate them.
Although this has previously been cited as a potential explanation for the 1961 event, there has been no evidence to support it until now.
"Here we show that plankton samples from the 1961 poisoning contained toxin-producing Pseudo-nitzschia, supporting the contention that these toxic diatoms were responsible for the bird frenzy that motivated Hitchcock's thriller," she writes.
A similar toxic bloom caused avian deaths in the same area in the 1990s, and in 1989 domoic acid was found to have contaminated mussels which killed four people on Prince Edward Island in Canada.
The spectacle of the dying birds was witnessed by Hitchcock, who took other elements of the film's plot from a Daphne du Maurier novel called The Birds.
- Independent