Mosman resident Andrew Brown said he was at Middle Head watching the sun rise with his four children when they spotted the lone whale entering the harbour and breaching about 7.30am.

Mr Brown said it made a turn and headed towards Manly at about 7.45am, just before the crew on board a Manly Fast Ferry service spotted it off the old quarantine station about 8am.

Bass and Flinders Whale Watching spokesman Richard Ford said the humpback came within 100 metres from Manly wharf, forcing one Fast Ferry to circle around it to berth.

"It's not unusual, they travel very close to the coastline up along South Head and that actually leads them into the harbour," Mr Ford said.

"Then when they head north and run into North Head they have to decide whether to go left or right and some of them turn left and go into the harbour.

"Then they realise it's getting shallower and they have to turn around and go back."

The crew on the final Manly Fast Ferry service of the morning reported that the whale was out of sight at about 9.30am, Mr Ford said.

Mr Brown said he and the children watched the whale breach the surface a number of times and spurt water high into the air.

"It looked like it followed a large container ship in through the heads," he said.