Thousands of dead fish washed up on Victoria's Ninety Mile Beach were probably killed by cold Antarctic water, according to the Environmental Protection Authority (EPA).

Many beachgoers had reported the dead fish between Seaspray and Marlo in Gippsland, identifying mainly the leather jacket species and also trevally.

The EPA said it was investigating but test results did not indicate water pollution was the cause.

It said the fish were most likely killed by cold Antarctic waters moving up the east coast.

The fish prefer warmer waters.

Large numbers of dead fish have also washed up on Tasmania's east coast.