The government has been warned that without controls, wilding pines could cover one fifth of all New Zealand's land area by 2035.
The warning came in a briefing to the incoming minister of biosecurity, Damien O'Connor.
These briefings come after every election and alert an incoming minister to the main problems that must be dealt with.
The briefing from Biosecurity New Zealand, which is part of MPI, said some progress had been made in dealing with wilding pines.
At the end of September, 226 people had been employed on a scheme to deal with them of a planned total of 550, costing $127 million.
The report argued wilding pines were a fire hazard, though they were usually criticised for displacing other species.
It warned the consequence of neglecting this problem could be serious.
Biosecurity New Zealand was much less anxious about Mycoplasma bovis.
It said although nearly 2000 farms had been affected, inspectors were finding less disease even though they were looking harder.
Animal tracing would cease next year and be replaced by background surveillance.
On another topic, the briefing suggested biosecurity legislation was not up to the task. It said the world had changed since the Biosecurity Act was passed in 1993.
Things were now being imported that were not even known about in 1993, it said, and climate change had transformed the risks of pests and diseases being established in New Zealand.
The Act is being reviewed.
Other comments in the briefing referred to several issues including new software for border controls and revision of the Government Industry Agreements, or GIAs.
There are 24 GIAs in place in New Zealand - they arrange for biosecurity costs to be shared between government and industry.