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Crowds lined Union Quay in the city centre to see the giant mammals who made their way up the river into the South Channel area.
The whales entered the inner harbour at about 2100 BST on Friday and began swimming up river towards the city centre.
Marine experts from University College Cork's Dolphin Research Unit are at the scene and are monitoring the situation.
They are not unduly concerned for the safety of the whales at this stage.
Worldwide population
They are hopeful the whales will be able to make their way to the mouth of the harbour with the tide.
Killer whales are regularly spotted in Irish waters, but it is very unusual for three of them to venture into polluted, narrow waters such as Cork Harbour.
The name killer came from sailors who saw the whales killing humpback whales and called them "whale killers".
 Killer whales regularly visit Ireland |
Over the centuries, the name has been switched to killer whale.
They prey mostly on fish, but also eat squid, sea turtles, seabirds and other whales.
Although the worldwide population is unknown, in the Antarctic alone there are about 180,000 killer whales.
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