The animal, thought to be a juvenile minke whale, is about 4m long. It was first seen on Thursday morning and seems to be healthy and content.
Minke whales are one of the most common in our waters. It is thought it may have swum in in pursuit of fish in the channel.
A fully-grown minke can grow to 9m in length.
The harbour authorities are liaising with experts in the Northern Ireland Environment Agency, and are expected to monitor the animal for several days in the hope it returns to open water.
There are no immediate grounds for concern over the animal's health, said the Department of Agriculture, Environment and Rural Affairs (DAERA).
"Minke whales frequent the waters around the mouth of Belfast Lough, but young or inquisitive animals will, on occasion, come closer inshore," said a spokesperson.
"However, our Marine and Fisheries team will continue to monitor the whale's behaviour in conjunction with colleagues from Belfast Harbour Commissioners.
"The animal is currently in a well-regulated area within Belfast Harbour where there is no risk of disturbance.
"The whale is not in an area that is easily viewable by the public, however, as a marine-protected species, people are advised to enjoy any views they are fortunate to have of this remarkable animal but not to approach or do anything to disturb it," the statement added.
A whale has been spotted in Belfast Harbour.