Individual licences may still be applied for, but they will be subject to “strict record-keeping and reporting requirements” and will be “closely monitored”.
A statement from Raeshaw Estate said it would appeal against the move.
“We share the frustration felt by many about Merrick’s disappearance but there is no evidence the estate or any of its employees were in any way responsible,” it said.
“The estate has zero tolerance for raptor persecution and remains fully committed to respecting wildlife, nature and the environment.
“Merrick’s last established position was not on land owned or managed by our estate.”
It added that no employee had been charged as a result of the police investigation.
“We welcome the presence of eagles on the estate, and we enjoy frequent visits from the species,” it said.
The action comes just a day after police appealed for information after a four-year-old golden eagle was shot elsewhere in the region.
The bird was discovered injured by a gamekeeper on an estate in Stanhope, near Tweedsmuir, on 15 January.