The NSW Department of Primary Industries (DPI) is investigating a fish death event in Killick Creek near Crescent Head.
"It is estimated that around 1000 Yellowfin bream, mullet, longfin eels and flathead have been impacted," a DPI spokesperson said.
Residents have raised concerns that the fish kill is partly due to current maintenance works on council's flood gates.
Council has released a statement assuring locals that similar work has taken place previously without causing a fish death event.
"While there is insufficient evidence to draw a link, or unequivocally rule out any cause, council have conducted similar works in the past without experiencing any associated fish kills," the statement said.
"At the same time, similar fish kills to the Killick Creek occurrence have been observed in the past which were found to be a result of rainfall following bushfires. As such, council is confident that the maintenance work was not responsible for the fish kill."
The DPI said the suspected cause of the fish kill is related to critically low dissolved oxygen levels generated following an extended period of drought and recent minor flooding.
"The drought has put the many river systems and creeks under extreme stress, and recent heavy rain in the region over the past week has further impacted water quality," a DPI spokesperson said.
"While widespread rain is a welcome relief, DPI Fisheries holds concerns around the potential short-term impact on fish and other aquatic organisms."
The resumption of flow in drying rivers brings with it risks due to poor water quality from built-up organic matter and sediment, which can have localised impacts on native fish species.
Despite these short-term risks, the resumption of flow and subsequent replenishment of refuge holes and connectivity along waterways will provide long-term benefits to native fish populations following the current drought period.
DPI Fisheries is working with Kempsey Shire Council and local residents to continue to monitor the situation at Killick Creek.
The NSW Government's $10 million commitment to support native fish during the current drought and bushfire season will be critical in assisting the recovery of populations when conditions improve.
Community members are encouraged to report any fish deaths or observations to Fishers Watch by calling 1800 043 536.
For more information on fish deaths, visit www.dpi.nsw.gov.au/fish-deaths
For more information on the NSW Government's Native Fish Drought Response, visitwww.dpi.nsw.gov.au/nativefish