Four East Gippsland properties near Tubbut and Orbost were searched on Tuesday as authorities hunt for those responsible for killing 136 of the protected species and four other native birds, recently found dead in the area.

The raids were carried out over a number of hours by a group of 45 officers from police and government agencies.

The confiscated evidence could be critical to cracking the case, Department of Environment Land Water and Planning investigations manager Iain Bruce said.

"A number of items were seized, including a four-wheel drive vehicle, two animal traps, phones, computers, documents, chemicals, unsecured ammunition and a number of additional native animal skulls," Mr Bruce said on Wednesday.

"One of (the skulls) is believed to be a wedge-tailed eagle.

"This was an important component of our investigation, in addition to the 136 dead wedge-tailed eagles and other birds recently seized from properties."

Experts plan to examine the skulls to confirm the species, Mr Bruce told AAP.

He previously labelled the investigation "the biggest case of wedge-tailed eagle deaths" in state history.

The "clearly intentional" killings, reportedly linked to poisoning, have caused community outrage and distress for investigators who searched 2000 hectares over three days to find the carcasses, Mr Bruce said.

But the chief investigator feared they may only be scratching the surface of the death count of the "majestic birds".

"The animals were hidden amongst bush and scrub, so it's not a definitive number," he said.

"It's not as though we have a mass grave or single point they've been hidden."

Public information has "continued to be valuable towards this investigation", but the department would not confirm if it sparked Tuesday's raids.

One person is still helping with inquiries, Mr Bruce said.

Wedge-tailed eagles are protected under the Wildlife Act 1975 and deliberately killing them carries maximum penalties of $7928, and a possible six months' jail, as well as an extra fine of $792 for each additional dead bird.

Australian Associated Press