A man has handed himself into police after a boat struck and killed a free diver in Melbourne's south-east yesterday.

A 41-year-old man from Carrum Downs contacted police and was subsequently arrested in Mordialloc today.

The victim, a 29-year-old man from Blackburn, had been spearfishing with a friend in Canadian Bay, off Mount Eliza, when he was hit by a recreational vessel.

According to police, the man’s dive partner surfaced and noticed a vessel operating nearby.

The man was treated on the Frankston Pier, but emergency crews could not resuscitate him. (9news)

Water police Senior Sergeant Alistair Nisbet said the victim’s friend spoke with the skipper of a boat from the water before discovering his friend in distress.

"He'd surfaced and he'd seen that (those on the boat) were close by to where they were swimming and he just wanted to make sure that they could see where they were," the sergeant said today.

The diver then discovered his partner had sustained serious injuries.

The diver and his partner were picked up by a passing boat, with police still searching for the vessel which struck the man. (9news)

Both divers were picked up by a passing commercial boat and taken to the Frankston Pier.

The diver was given CPR by paramedics but died at the scene.

His partner, also aged in his 20s, was not injured.

Snr Sgt Allister Nisbit described the pair as “experienced ski divers," who were "using buoys and floats and flags” to alert water users they were diving in the area.

Snr Sgt Nisbit said police closed off a number of boat ramps and had collected a significant number of boat registrations of vessels leaving the water.

“There was a fair bit of boating traffic yesterday,” he said, saying it would take investigators some time to work through the list of vessels.

“We are calling out for witnesses that were boating in Canadian Bay yesterday at around 1pm if they saw any divers, or diving flags in the area,” Snr Srg Nisbet said.

A speed limit of five knots (9km/h) applies to boat operators on all Victorian waters within 50 metres of swimmers or 100 metres of a diving flag.

A diver has been struck and killed by a boat near Frankston. (9news)

Snr Sgt Nisbet urged people using the water to take care and be aware of activities happening above and below the surface.

“There’s a huge responsibility on boat operators out there, days like yesterday when it’s nice down the bottom of the bay,” he said

“It’s your responsibility as a vessel operator to ensure you operate safely.”

Australian Volunteer Coast Guards spokesman Jeremy West said it was unlikely the skipper would have been unaware of the collision.

"It's usually fairly obvious that you've hit something, particularly a solid object," he told ABC radio today.