The existing fruit fly quarantine area in the Riverland will be amended to include fire blight restrictions.
"This isn't about halting free trade. It's about protecting SA horticulture and jobs," the minister said.
"If we limit it to a tight quarantine zone over those areas, we believe that the quarantine zone proposition could not be challenged in the courts.
"They will be a quarantine zones similar to the fruit fly quarantine zone in the Riverland, you will not be permitted to take apples and pears into those areas."
The government will try and exclude large regional centres but where it can't, retailers will be asked to ensure the fruit they sell comes from disease free areas.
Apple grower Michael Stafford has welcomed the proposed quarantine areas for the state industry that is worth $80 million at the farm gate.
"Fire blight will have a devastating impact on my business and the state, whichever state it was found in, it would mean you would be excluded from the rest of the markets in Australia and potentially overseas as well."
-AAP