A man who rammed a great white shark with his boat and then beat it to death with a metal pole has been ordered to pay nearly $20,000.

Justin Adam Clark was prosecuted by the New South Wales Department of Primary Industries (DPI) over the death of the juvenile shark at Sussex Inlet on the south coast in January 2012.

He was found guilty of harming a threatened species in Wollongong Local Court.

Great white sharks are protected throughout Australian waters, though the Federal Government has granted an exemption for the Western Australian Government to cull large sharks.

Witnesses told DPI officials the 40-year-old man, from Glenbrook in Sydney's west, chased the shark in his boat after it was seen in the area.

He herded the animal into shallow water, deliberately using his boat to hit the shark several times.

DPI says the main injuries to the shark were caused by the boat's propeller.

A rope was tied to the shark's tail and it was towed back to a boat ramp with help from a second boat.

The juvenile shark was dragged up a boat ramp before being beaten in the head with a metal pole. ( NSW Department of Primary Industries )

The department says the shark was then bludgeoned to death with a metal pole.

The magistrate ordered Clark to pay a fine of $8,000, plus costs of $10,103.

The man in charge of the second boat that helped drag the shark to shore also pleaded guilty to harming a threatened species and was put on a six-month good behaviour bond.

DPI director of fisheries compliance Glenn Tritton says ignorance is no excuse for harming a protected species.

"This conviction sends a strong message that harming of our threatened species will not be tolerated," he said.

"The low population numbers following historical exploitation, plus their low reproductive rate, long gestation and late age at sexual maturity lead to slow recovery of the great white shark population and demonstrate the need for its protection."