The National Parks and Wildlife Service says over 600 of them were found dead in the Bruskey/Erne River at Killydoon, near Ballinagh.
Other fish and freshwater animals haven't been affected.
Early test results indicate a crayfish plague may be responsible.
Inquiries are focusing on how the disease got into the river and whether it may have been passed on through fishing equipment used in affected waters in the UK or elsewhere, or if non-native species may have been introduced to the area and transmitted the disease onto the crayfish.
