Aberdeen Coastguard said the alert was raised close to the entrance to the port shortly after 08:00.
The animal had broken free while being loaded onto a transport float.
The cow was shot by police marksmen about five hours later. Police Scotland said humane destruction was a "last resort" but public safety and animal welfare had to be a priority.
The cow was starting to be swept away when the decision was taken to shoot it.
A NorthLink Ferries spokesperson said: "The animal was being loaded onto a road transport float when the incident occurred."
An Aberdeen Harbour spokesperson said the port had remained open, with vessel entry being taken on a "case-by-case basis".
An animal sanctuary had offered to take the cow if it had been possible to rescue it.
A cow which got into the water at Aberdeen Harbour has been shot after a rescue effort failed to coax it ashore.