New Zealand has strict controls around genetically modified organisms and it is illegal to import, develop, field test or release a genetically modified organism without approval.
"We have no evidence to suggest the GM material was deliberately brought into New Zealand," Thomson said.
"The importer concerned was unaware of the GM content of these seeds and, as soon as they became aware of the possibility, they contacted MPI. We applaud them for that.
"This is a global situation, many other countries are dealing with the same issue and MPI is working closely with our overseas counterparts.
"It seems that no authorities anywhere in the world were aware that these varieties of petunia contained or were bred with GM plant material."
MPI was tightening its controls at the border to require all petunia species imported as plants or seeds to have a GMO certificate stating they are GM free before being allowed in.
"Given that it's winter, it is unlikely there are many plants currently in circulation and the risk of these plants becoming established is negligible," Thomson said.
"Petunias are often grown as annuals, so they complete their life cycle in one year.
"They also do not set seed efficiently, so their ability to grow in the wild, shed seeds and spread is negligible."
MPI was also working with industry to trace and destroy all seed stock and unsold plants existing in New Zealand.
"We have made it clear to businesses holding the suspected GM petunia varieties that they must not be sold, and therefore will have to be taken off the market.
"While these plants and seeds do not present a risk, they do not have regulatory approval, this means it is an offence to knowingly plant or otherwise propagate them.
"Any existing stock will be destroyed."
The varieties identified as GM and currently known to have been imported into New Zealand are marketed under the names African Sunset (an orange-flowered variety), Trilogy Red (also known as Diva Red) and Trilogy Deep Purple (also known as Diva Deep Purple).
Anyone who may have purchased petunias with these variety names were asked to remove the plants or seeds and dispose of them in their rubbish, and not in their compost or green waste.