A man has been charged over the deaths of more than 100 wedge-tailed eagles found poisoned in Victoria's far east.

The 136 dead birds were discovered on a property at Tubbut, in far east Gippsland near the New South Wales border, in April.

It is alleged he used poisoned baits to kill the protected birds between October 2016 and April 2018.

The ABC understands he is not the owner of the Tubbut property involved.

He is facing two charges under the Wildlife Act 1975 and has been released on bail to face court at a later date.

The man was charged after a state-wide investigation involving more than 30 people.

The eagle carcasses were found in bushland and scrub on properties that covered about 2,000 hectares.

Victoria's Department of Environment Land Water and Planning (DELWP) said it was the largest case of wedge-tailed eagle deaths in the state's history.

"We would like to inform the community that investigations are ongoing, including forensic examination of evidence recently seized during searches of relevant properties," a spokeswoman said.

The deliberate killing of that many wedge-tailed eagles carries a maximum penalty of up to six months' imprisonment and fines totalling about $115,000.

The protected species are Australia's largest bird of prey.