MICK Fanning has been pulled from the water at Jeffreys Bay after a three-metre great white shark appeared in the line-up.

The shark incident is the second in two days at the notorious South African break, where Fanning was attacked in the J-Bay Open in 2015.

Surfing in the event's quarter-final, Fanning and fellow competitor Gabriel Medina were pulled from the water as the heat was put on hold after the great white was spotted moving towards the surfers from around 700 metres away.

Fanning, who would eventually lose the heat to Medina, saw the footage for the first time when he was recapping the quarter-final, and said he was stunned by the "huge” shark.

"Look at that thing, that thing is a beast, at least they saw this one. I am glad they got us out of the water,” Fanning said.

"Those things are just submarines, however long they are, the roundness of them as well ... they are big, big beasts.”

Fanning, who famously punched the shark that attacked him just two years ago, said he didn't panic as response and safety teams placed the athletes onto boats and monitored the shark as it exited the line-up.

However, Fanning said while he was content to enter the water, he also saw the irony of lightning very nearly striking twice once he was clearly to safety.

"I'm really glad they got us out of the water but I felt really safe out there with the skis, the drones and the plane so it was an easy decision to paddle out,” he said.

After discussion with the WSL's Commissioner's Office and the athletes, competition resumed and Fanning's attempt at winning a second consecutive J-Bay Open title and a fourth overall was ended by 2014 world champion Medina, who was superior in advancing to the semi-finals against Portugal's Frederico Morais.

"We had a slow start to the heat and I made a few mistakes but Gabe (Medina) is just surfing so well at the moment, so it was a tough heat,” Fanning said.

"It's been such an incredible contest though. I think we've seen some of the best surfing to see how many 10-point rides have gone down. What else could happen here?”

The shark incident follows on from that of two days ago, when a mako was spotted just 90m from Brazilian Filipe Toledo and Sunshine Coast surfer Julian Wilson, who famously came to the aid of Fanning when the pair were in the water during Fanning's 2015 attack.