A desperate search for a 25-year-old man is under way after a boat flipped off Victoria's Mornington Peninsula coast late last night.

A five-and-a-half metre fibreglass boat with two fishermen on board overturned around one kilometre offshore of Mornington, according to police.

Emergency services were called to Schnapper Point Drive about 11.15pm.

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One man was rescued by another boat.

He was assessed by paramedics and was taken to hospital with hypothermia.

An immediate search commenced involving Water Police, Air Wing and Uniform officers, with assistance from HEMS, Life Saving Victoria and the coast guard.

It continues this morning.

Police are investigating whether a potential wake from another vessel caused the boat to capsize.

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