I think the main problem here is that the NAFS is part of MPI. As stated in the article:
[NZFS] should not be within the same organisation that is charged with promoting New Zealand's primary producing export market. It doesn't make any sense to be nested in there.
They could have a synergistic relationship; but if there is a breach...MPI will err on the side of more exports, where NZFS should err on the side of safety and food system integrity.