The facility employs five employees, and is involved in rebuilding the salmon stock in Nova Scotia.
Councillors with the Region of Queens were unhappy with the decision, and expressed their frustrations during regular council on May 22.
Coun. Mervin Hartlen expressed disbelief federal government would fund the Afghanistan military for four years, but not things on own soil.
"We're going to spend $110 million a year to fund a foreign military, but we can't keep a fish hatchery open. It's just ridiculous," he said.
Council approved a motion to send a letter in protest to MP Gerald Keddy, and the Minister of Fisheries and Oceans.
The hatchery has operated as a genetic bank for fish in the Atlantic region for quite some time. Salmon would be raised that genetically match ones that swim up the Medway River, among others. After releasing the fish into the ocean, they would later return to the river they were genetically matched to.
Department of Fisheries and Oceans (DFO) communications manager David Jennings says they will likely consolidate the work at another facility.
Part of the closure is because of a recommendation that there is no longer a need for captive rearing of Atlantic Whitefish. The Mersey facility also was involved with that project as well.
Mélanie Carkner, media relations advisor with DFO, says this and other changes they have made in DFO and the Canadian Coast Guard will save $79.3 million.
