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Cordons are in place at Meola Creek in Westmere where the man's body was found in the water about 7am today.
A police spokesperson said inquiries were being made to establish the circumstances of the death, which was currently being treated as unexplained.
The public is asked to avoid the area.
Police would like to hear from anyone who has see or heard anything unusual in the area overnight or early this morning.
• Contact police on (09) 302 6557.