Justice Toogood ruled in the High Court at Auckland that ancient swamp kauri was not subject to the Protected Objects Act and its export could continue.
He said imposing extra restrictions would "create an oppressive regime restricting the removal from New Zealand, by ordinary travellers, of everyday products which have no particular significance".
He also refuted the society's argument that buried swamp kauri was a fossil worthy of protection under the act, like kauri gum and scrimshaw whale bone.
Justice Toogood noted there had been historical concern around the export of kauri stumps but he was satisfied with MPI's current system which he said had "progressively improved its procedures" since late 2011.
Ms Furrell said the group would now consider whether to appeal the decision to the Court of Appeal.
NEPS took some heart in the judge saying the group had brought a valid case and therefore he would review whether to charge the group costs of the case or have MPI cover them.
Northland-based Green MP David Clendon said the export of unworked timber was a "lose-lose situation".
The rate at which swamp kauri was being extracted was damaging Northland wetlands - which, as well as being home to native plants and animals, contributed to flood protection and water quality - but also came at a social and economic cost.
Though rare and unique to Northland, swamp kauri was being treated as a cheap resource, Mr Clendon said.
"We should be treating it as scarce resource for our artists and craftspeople to turn into high-value artefact's that people will want and cherish. Instead we're exporting truckloads of slabs"
In coming to his decision the judge had taken a "fairly narrow interpretation" of the law, he said
A different judge on a different day could have come to a different decision, Mr Clendon said.
If the Greens were in government they would look at changing the legislation and bringing more specific protection for swamp kauri, he said.
