The Kiwi has this week suffered a relapse of the injury that was flared by a qualifying crash at this week's Clipsal 500.
Murphy is not expected to be back behind the wheel until September's Sandown 500 – ruling him out of commitments in both the V8 Supercars Championship and New Zealand V8 SuperTourers Series in the meantime.
It is expected that both Kelly Racing will announce their plans to replace Murphy early next week.
Murphy, who skipped April's Symmons Plains V8 Supercars event following an initial operation, says further surgery was his only option.
“Despite the discectomy procedure I had after Clipsal, the disc has continued to rupture and I've been in a fair amount of pain and discomfort this week,” said Murphy in a statement.
“I need to get the vertebrae fused to sort this once and for all and while it means I'll be out of the car for the next three months.
“I expect to be 100% and back racing for the Pepsi Max Crew here in Australia and Mike Pero Racing in New Zealand by the end of September.”
While highly disruptive to his racing programs, Murphy emphasised that his back problem is not a career-ending injury.
“It's obviously not ideal – being out of the car is never good in motorsport, but Kelly Racing and all my
sponsors on both sides of the Tasman have been incredibly understanding and supportive,” said Murphy.
“My medical team has assured me that I will have no lasting effects from this operation which is expected to fast track a full recovery.
“I need to focus on my operation but I know contingency plans are already well under way for the rounds ahead and would expect announcements on who will fill in for me while I am out of action very soon.”