Zak, owner of the Mohawk Trout Hatchery, had pleaded guilty on March 26 to two counts of violating the Migratory Bird Treaty Act and one count of conspiracy.
His attorney, Vincent Bongiorni, said then his client was not willing to accept a guilty plea for the eagle charge.
"There was a factual basis to support those two counts and our claim is that it doesn't support the bald eagle count," he said.
Zak's employee, Timothy Lloyd, 30, of Easthampton, pleaded guilty March 23 to two counts of violating the migratory bird act and one count of conspiracy.
Federal investigators said they found more than 250 great blue heron carcasses, as well as carcasses of ospreys and a bald eagle on hatchery property. Tests showed the birds were killed by gunshots.
U.S. Fish and Wildlife Service agents say they staked out the hatchery periodically and saw Zak shoot at a heron with a scoped rifle and Lloyd shoot and kill an osprey.
The men are to be sentenced on June 27. Zak faces up to three years in prison and Lloyd faces up to 18 months.