A kookaburra, ravens and a raptor were also found dead.
Silvester was the one who alerted the authorities to the deaths in May 2018, after he stopped working at the farm due to an argument with his boss, farm owner John Auer.
He also reportedly named others involved.
Prosecutors say others are being investigated over the killings but have not been charged.
According to Department of Environment, Land, Water and Planning (DELWP) prosecutor Chrisanthi Paganis, most of the eagles died after being poisoned with the chemical Lannate.
Three different chemicals were used to kill the animals.
"John Auer showed him how to do it by injecting the substances into the necks of lambs," Paganis told the court.
Eagles would then feed on the sheep and lamb carcasses and die within 30 minutes of ingesting the chemical.
"He knew it was unlawful to kill them," the prosecutor told the court, quoted by ABC.
"His actions were conscious, voluntary and deliberate, he googled them, he knew they were protected species."
According to Defence lawyer Keith Borthwick, the Kiwi farm worker was under pressure to increase lamb survival rates.
Borthwick also said the matter was only taken before the court before the case against his co-accused was completed because they feared Silvester was planning to return to New Zealand.
Court reportedly told Silverter he would have received a harsher sentence if he had not pleaded guilty.
Silvester asked to address the magistrate in court and said: "[The] Wildlife [department] have lied, they told me it would only be a fine. I just want to put this behind me and go home."
"You'll be back home in New Zealand in a month," the magistrate responded.
