An MPI spokesman confirmed charges had been laid against two people under Operation Silbae. He said the matter was before the courts and no further details could be released.
Papers at Wanganui District Court show each of the Higgies had elected trial by jury on one or more charges.
The couple made and run Paloma Gardens, near Fordell, Wanganui's only Garden of National Significance. It includes a huge collection of plants and trees from all over the world.
The two are well known in botanical circles, and Mr Higgie is an expert on Araucaria, the plant grouping that includes the New Zealand kauri and Agathis silbae, one of the plants the Higgies have been charged with possessing.
Mr Higgie faces a total of six charges. Three are to do with a small Ficus watkinsiana (strangler fig) plant found growing on a hot pad at their garden in February 2012. His wife is separately charged with the same three. The plant has since died, he told the Chronicle.
The charges over the Ficus are of possessing it while knowing it was unauthorised, importing it and failing to notify MPI about it.
Mr Higgie also faces three charges in relation to Agathis silbae, a Pacific Island relation of the kauri. They are of possessing the unauthorised plant, importing it and failing to tell MPI.
Agathis silbae has been the subject of controversy, with some botanists saying there is no such species.
MPI and police pursuing Operation Silbae subjected the Higgies, Auckland ecologist Graeme Platt, Auckland Botanic Gardens and the gardens' curator Jack Hobbs to dawn raids in 2012.
The raids were looking for evidence of Agathis silbae, and charges have also been laid against Mr Platt.