After consultation with coaching and medical staff, Magnussen has elected to go under the knife early to ensure he has the best run possible towards Rio, even if it means missing out on defending his twin-100 metres freestyle crown at the worlds.

The lure of being the first man to win the blue-chip sprint for three consecutive world championships was a motivating force for the 24-year-old but he has bigger fish to fry at the Olympics, where he remains determined to fire after the disappointment of London 2012.

Magnussen won the gold medal at Glasgow's Commonwealth Games last year but has struggled to retain his world-beating form, with Dolphins teammate Cam McEvoy claiming his scalp on a number of occasions as Magnussen battled with his injury.

Doctors have now revealed the reason, with the damage to the sub-scapular region of his left shoulder causing it to lose 70 per cent of its strength.

Given the explosiveness required for sprint swimming, it has been a significant factor in losing the fluency of his stroke as he slipped to world number three. Doctors gave the news to Magnussen, as well as his coaches Mitch and Lach Falvey and Swimming Australia, the news on Friday.

"We, as a team, have explored every possible avenue to allow me to compete but unfortunately surgery is the only viable option if I am to be fit for the 2016 Rio Olympics," Magnussen said.

"I will now focus all my time and effort on preparing for the Olympics next year. I am looking forward to regaining full strength in my shoulder and getting back to my best performances."

Dolphins head coach Jaco Verhaeren said the advice was that Magnussen get treated sooner rather than later to prevent further damage.

"It is tough when a swimmer gets to this point and has to withdraw from the national team," Verhaeren said.

"All indications from our medical staff are that surgery is the best option. If there are any further issues then they can be treated sooner rather than later."