The messages from a Gippsland land owner congratulating his employee for killing dozens of wedge-tailed eagles have been revealed after the businessman admitted to his part in the scheme.

John Franz Auer's farm manager Murray Silvester injected the carcasses of lambs, sheep and kangaroos with insecticide to use as bait to kill eagles over about two years.

Environment Department officers discovered at least 134 dead wedge-tailed eagles, along with the carcasses of four other protected bird species on Auer's properties in May and June last year.

"I just wouldn't have dreamed of those numbers. Bloody well done," Auer said in messages to his farm manager.