A desperate search is taking place off the coast of southeast Melbourne following the disappearance of a man who was on a boat that capsized.

Emergency services learnt about the missing man at about 11.15pm on Friday.

Police believe the boat capsized about 1km off shore, near the Mornington Pier which is about 45km south of the Melbourne CBD.

An immediate search took place and one man was rescued by another boat and assessed by paramedics but was not seriously injured.

The search resumed on Saturday to look for the second male occupant of the vessel, who remained missing.

The missing man is believed to be in his 20s.

The large-scale search team has consisted of water police, helicopter and uniformed police officers, Life Saving Victoria, the coast guard and a Helicopter Emergency Med

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