MPI was also presented with a summary of new analysed test results from an industry science group.
"This information showed that the definition for identifying multifloral mānuka honey was initially set too conservatively and would exclude legitimate multifloral honey," Bryan Wilson, MPI's deputy director-general regulation and assurance, said.
NZ Beekeeping president Russell Berry said the ministry had not taken enough notice of submissions put forward by his association, which represents 300 beekeepers, and the UMF Honey Associations, which oversees all use of the UMF quality trademark, in the leadup to the change.
Berry said the requirements, if left intact, would have cost members $100 million in lost export earnings.
"At the 11th hour, they changed definition of manuka honey very substantially, which meant a lot of manuka honey would not have met the rules to be exported," he told the Herald.
Multifloral manuka honey is only partly derived from the manuka flower.
Under the unrevised rules, manuka honey with a UMF factor of 5 to 10 would have failed the test, and would have had to have been exported as "amber" honey.
Berry said today's U-turn from MPI was "a perfectly reasonable result."
Apiculture New Zealand said it welcomed MPI's decision to adjust its mānuka honey science definition for multifloral honey.
"We're pleased that MPI has listened to industry and delivered a definition that ensures our consumers can continue to have access to good New Zealand multi-floral mānuka honey," Apiculture NZ chief executive Karin Kos said in a statement.
"The definition also gives our industry certainty for the 2018 honey production season," she said.
The implementation date of the notice remains February 5.