The vessel started taking on water Thursday morning, said the coast guard's assistant commissioner for Atlantic Canada, Wade Spurrell.
He said the crew was on fishery patrol outside the 200-mile limit when alarms alerted them to water leaking around the ship's propeller shaft, and the decision was made to return to port.
It's unclear how much water got into the vessel.
Pumps were used to get rid of the water and they were subsequently shut off. No further water has been reported getting into the ship.
Starting Thursday evening, Spurrell said an offshore supply ship, Atlantic Kingfisher, met the vessel to escort it back to St. John's
The coast guard ship Sir Wilfred Grenfell was also called to assist with the vessels and accompany the Cygnus back to port.
Spurrell said the 21 crew are safe and the situation stable.
"We've got everything lined up for the vessel's arrival, and we hope to get on this as quickly as we can and determine the cause and start to address the problems," said Spurrell.