"We ask that the public not dispose of plant material or seeds in compost or green waste," Mr Thomson said.
There was no evidence to suggest the GM seeds were brought into country deliberately, he said.
"As soon as (the importer) became aware of the possibility, they contacted MPI. We applaud them for that," he said.
The ministry would be introducing new border controls requiring all petunia seeds to be certified GM-free.
"This is a global situation, many other countries are dealing with the same issue and MPI is working closely with our overseas counterparts," Mr Thomson said.
"It seems that no authorities anywhere in the world were aware that these varieties of petunia contained or were bred with GM plant material."