"If the doc says it's time to retire, those will be the cards I'm dealt and I'll accept it," the Queensland Reds veteran told the Brisbane Courier-Mail.
"I'm taking a break to give the body a rest from playing and all contact training.
"Obviously, there may be a big decision where things lead but I'm not a doctor.
"I'm a footballer with my family as No. 1 and I'll follow advice to the letter from the very good medical people around me."
Flatley, who won't play against the All Blacks on September 3, has suffered from blurred vision and has had two previous concussive episodes.
He visited a concussion expert in Melbourne this week as well as being examined by eye specialist Mark Loane, a former Wallaby captain.
Flatley will be further evaluated next month.
Wallaby coach Eddie Jones said the fly-half was "highly unlikely" to be available for the European tour in November.
"Our main concern has always been for Elton's health and the advice suggests he needs to take a break from the game," Jones said.
"The earliest we would see him back is in Super 14."
Flatley said his Test-night withdrawal against South Africa in Perth last weekend was tough to take.
"It was gut-wrenching to pull out 15 minutes before a Test you'd prepared all week to play," he said.
"I knew my vision wasn't 100% after making a few tackles on the bags in the warm-up."
Flatley admitted there was "a fear of the unknown" with concussion.
"It's not like a knee ligament where you can say you'll be right in four weeks," he said.