Anglers on the Murrumbidgee and Murray rivers are pulling in fish filled with up to 20 mice.
Lavington's Compleat Angler owner and The Border Mail columnist Russell Mason said there had been widespread reports and fears it may pose a risk to nearby waterway ecosystems.
"When you see the numbers of mice these fish have in them, it certainly could knock the cod around but not only them but the bird life as well," Mr Mason said.
"It's a bit of an unknown quantity.
"If the mice have been poisoned I don't know how long it takes them to die and if in the meantime they're swimming across the river and being taken by the cod will it kill the fish?
"There's still a bit of a question mark around it to be honest."
It has been reported thousands of mice are being gorged by fish in the Dubbo region while attempting to swim across rivers.
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Mr Mason said the Lachlan and Darling Rivers may also soon see a rise in fish eating poisoned mice.
Generally secondary poisoning in animals that have eaten baited mice is unlikely, unless consumed in large quantities.
CSIRO mice expert Steve Henry said mice have continued to present in larger than usual numbers around cropping areas.
"As the rice harvest has progressed we've been hearing more and more reports of high numbers of mice," he said.
"From Echuca through to Barham they've been recording high numbers for two or three months now.
"Generally through the cropping zone there are higher numbers than normal."
Mr Mason said that it isn't unusual for cod to eat mice, particularly when there are so many about.
"They eat just about anything anyways, so there's not a problem with them eating mice generally but certainly if they do eat those poisoned mice it could create a major issue," he said.