Council animal control officer Murray Malloch said dog control staff would be policing the cycleway in future to ensure dogs were being kept on leads. Owners who let their dogs run free could be slapped with an infringement notice.
Pets could be left to run free on the beach, but not the cycleway.
"We will pick portions (of the track) to police," he said.
Mr Edwards said the penguins were returning to their nests before breeding. In the worst case scenario, a bird would be killed, leaving the chicks or eggs to die, stopping the colony from reproducing that year.
"It brings the entire colony at Karoro under threat.
"Don't let your dogs roam at night."
Mayor Tony Kokshoorn, who lives close to the Karoro beach, said that about five years ago his family often saw 18 or 20 birds on the beach at the mouth of Watsons Creek.
Since the cycleway had gone in, the penguin environment had changed and there were now "half a dozen, at most".
"You can still hear them at night," he said, but from his observations the colony appeared to be under threat.
- The Greymouth Star