This is the most visible right whale visit to the harbour this year, another whale also having been reported to be briefly just inside the harbour mouth, near Shelly Bay, on July 29.
Crew aboard the wildlife cruise vessel Monarch gained good views of the whales yesterday, including just beneath the Harington Point gun emplacements.
After spending some time in the area, the whales apparently left the harbour about 3.45pm.
The 5.5m-long Department of Conservation vessel, Coastal, skippered by Doc ranger Rick Ratcliff, and with Doc programme manager for biodiversity David Agnew aboard, later located the whales southeast of Taiaroa Head about 5pm.
Doc marine ranger Jim Fyfe, who was also aboard, said one of the whales was "certainly pretty spectacular", leaping into the air and at times holding its tail high out of the water.
Mr Fyfe advised people to keep an eye out for more whales off the Otago coast, and to report them to Doc via its free hotline: 0800 DOC HOT.
Three other right whales were reported at Kuri Bush, north of Taieri Mouth, at 8.45am yesterday and whales were also sighted near Bull Creek, South Otago, about 6pm.
University of Otago marine science research fellow Dr Will Rayment, who is undertaking a study of right whales, yesterday took photographs of the harbour whales from the Doc vessel.
Hunting of southern right whales nearly wiped them out in the 19th century, and the whale population has since been recovering at the Auckland Islands.
Further whale sightings in Otago waters were "great news" for the whales and also provided "fabulous" views, Dr Rayment said.