Muir said the sector is at a “critical juncture as it adjusts to the reality of recurring blue-green algae blooms” on the lough.
“I am pleased that we have been able to offer support and my officials are moving to get this financial assistance to the industry at this difficult time,” the minister said in a statement.
He said it will allow the sector to consider how it will adapt to the challenges it faces, and he would “encourage them to use this time to identify new markets and introduce measures to improve the management of eel stocks”.
“The situation impacting the Brown Eel Fishers has been a stark reminder of the human cost of the Lough Neagh crisis, and we must collectively work to turn the tide on water pollution in Northern Ireland,” he said.