The organisation that supplied them, the Clean Plant Centre North West (CPCNW), in Prosser, Washington State, was then struck off the list of approved suppliers.
MPI said it had two new standards for domestic and foreign producers of plant varieties almost ready for release, with one of them slated for this month.
In a statement, the Ministry said the seized material had been tested for disease, found to be clean and returned to the growers who had owned it.
In the aftermath of the original seizure, several growers went to court seeking compensation for the impounded cuttings.
One of them - Andy McGrath, who is seeking $4.2 million - said MPI's comment dealt with only part of the problem.
"The statement is accurate as far as it goes," Mr McGrath said.
"But the border is still closed, MPI have not released two shipments [of plants] and they are avoiding the issue of compensation."
Kerry Sixtus of Taradale was seeking $1 million, which he said was a conservative estimate based on lost opportunities for developing new lines of fruit, along with actual material losses.
Mr Sixtus added that even though there were many popular and delicious types of fruit available in New Zealand, companies like his had to be always on the lookout for new varieties.
"We are talking a long-term game, here, we are not talking tomorrow," he said. "So what we bring in today, you are going to see in ten years time."
Mr Sixtus said the orchard industry was competitive today but had to stay ahead of the game.
"If we miss one or two varieties at the wrong time, Chile picks it up, Argentina picks it up, and our growers might miss a big opportunity."
MPI said it was working on new guidelines and had been in touch with the American centre in Prosser.
It would visit the centre as soon as the new rules were published and the American centre said it was ready to be audited.
Mr McGrath said that could not come soon enough.
"The Washington State facility at Prosser is a clearing house that everybody in the world uses," he said.
"It is extremely important, it is the global clearing house for new material."
- RNZ