Any apple consignments that did not meet Australia's import requirements would be rejected, Dr Emerson said.
The system will be audited and verified by Australian authorities before the apples leave New Zealand, and Australian quarantine officers will inspect all consignments when they land in Australia.
Opposition Leader Tony Abbott told reporters in Canberra there was no certainty disease would not get into Australia with imported apples.
"That's what we are calling on the government to ensure - that no diseased apples come into this country - and we are far from confident that the Australian quarantine service at the present time can do that," Mr Abbott said.
Apple and Pear Australia chairman John Lawrenson agreed, saying all Australian growers should now fear the appearance of fire blight, leaf curling midge or European canker.
"Farmers will be nervous just getting out of bed in the morning because they will be wondering if today is the day they discover fire blight in their orchard," he said in a statement.
He described Biosecurity Australia's quarantine protocols as "horrendously weak".
An opposition private member's bill to give parliamentarians a veto over apple import permits will be introduced on Monday.
Dr Emerson said continuing to block NZ apples from the Australian market could lead to trade restrictions affecting other Australian industries.
"Australian farmers would be exposed to retaliation by New Zealand," Dr Emerson said.
The battle began five years ago when NZ took an Australian risk analysis on apples to the World Trade Organisation, arguing it was unfair.
The WTO ruled in late 2010 that the Australian quarantine restrictions were not supported by science.
Australian authorities then reviewed quarantine policy, sought industry comment and came up with the new import conditions.
- AAP