Leigh Nairn said his drone was badly damaged in the incident at Binnu, 550km (340 miles) north of Perth.
The drone, used to monitor barley-seeding equipment on his property, was sent off to be repaired.
He said he was "100% lucky" that the drone managed to capture an image of the bird as it swooped.
"That's the only photo I have of it," he said.
"I'm not sure where it came from, but I was obviously in the wrong spot and [it] wanted to let me know that."
The eagle flew off unscathed, he said.
