Scotland Yard said the discovery was made by a member of the public in Regent's Canal in Hackney, east London, yesterday afternoon.
It comes more than six months after the headless and limbless body of actress Gemma McCluskie, 29, were discovered in the same stretch of water.
Miss McCluskie, who played Kerry Skinner in the BBC soap in 2001, had been missing for a week after attending the £650 million opening of the new Royal London Hospital in Whitechapel, east London.
She was last seen returning to the home in Pelter Street, Hackney, that she shared with her brother Tony McCluskie.
A police spokesman said: ''We can confirm that a head was recovered from Regent's Canal yesterday afternoon. It is still yet to be identified.''
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The spokesman would not speculate on a connection with the killing of Miss McCluskie, whose remains were found in March.
Friends launched extensive searches across east London in a bid to find her, and former EastEnders co-stars Natalie Cassidy and Brooke Kinsella both appealed for help on Twitter.
McCluskie, 35, is due to stand trial accused of the murder of his sister on November 12.