A 12-year-old boy who has been missing in rough waters off a popular surf beach in Victoria has been presumed dead.

Danny was with his family when he disappeared while swimming at the unpatrolled No 4 Beach in Venus Bay, around 120 kilometres south-east of Melbourne, at 11.30am on Sunday.

Two days of searches have failed to find him, and police have now shifted their efforts to a recovery mission.

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Danny, whose last name wasn’t supplied by police, is presumed dead. (Victoria Police)

“Due to the length of time Danny has been missing, police are now working to recover his body,” police said in a statement today.

Acting Senior Sergeant Matt Wade has previously said the boy’s family are “obviously distraught”.

Police are continuing to scour the 25km stretch of coastline at Venus Bay and the surrounding areas.

Their efforts have been supported by local officers, the police helicopter, water police, the coast guard, SES, Life Saving Victoria, and members of the public.

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Boy, 13, saves two teenage girls from dangerous rip at Venus BayVenus Bay is a 25km stretch of coastline. (9News)

There are five main surf beaches along Venus Bay, with all but the first unpatrolled.

The beaches, numbered one to five, are known for having large surf, strong currents, rips, and constantly changing conditions.

The east coast town has a tiny population of 500 people, which surges into the thousands when surfers, anglers and families arrive for the holiday period.