"Having considered all the issues raised, I have now formed the opinion that MPI should not have extended timeframe for responding to your request," Donnelly wrote.
"I have recommended that MPI apologise to you for the decision."
Forest and Bird's Central North Island regional manager and kauri dieback spokeswoman Rebecca Stirnemann said her group had been working with leading kauri dieback and biosecurity experts for many months and received several reports about "mismanagement" by MPI, particularly in the areas of research and community engagement.
"For example it appears that high priority areas of research have not been answered, some not even procured yet, or if so very piecemeal or very poorly funded."
Among other requests, the group asked MPI for research, advice, reviews and communications around its management of kauri dieback.
The MPI eventually responded with eight files of documents, totalling nearly 80MB in size, which Forest and Bird was now trawling through.
"For the Ombudsman to now instruct a government department to apologise for withholding information is a strong signal that this culture of secrecy and obstruction has to end," Stirnemann said.
"MPI should be deeply embarrassed, and their new ministers must ensure there is a major culture change at all government departments and agencies towards openness, and transparency, and access to information."
This afternoon, an MPI spokesperson told the Herald it was not able to respond within the required timeframe, but "released the information to Forest and Bird immediately after it was ready, as is usual practice".
"We received the Ombudsman's decision a few days ago and will be considering it and providing a response to the Ombudsman and Forest and Bird in due course.
"I'm sure you'll appreciate that we would provide this response to Forest and Bird before giving it to any other party."
The spokesperson said MPI took its responsibilities under the OIA seriously and had a good record of answering queries in time.
In the first six months of 2017, the MPI responded to 782 requests under the OIA, with 95 per cent of these being issued on time.
It comes as the Government is to hold a review into the eight-year-old programme responding to kauri dieback disease, with the Minister of Forestry Shane Jones calling previous efforts "grossly substandard".
MPI director-general Martyn Dunne had advised that the best course of action was to create a national pest management strategy and treat the disease as a major biosecurity threat, Jones said.
Organisers of the Hillary Trail Marathon have also cancelled February's event in the Waitakere Ranges, saying they need to respect the local iwi Te Kawerau a Maki's request to support the rahui placed this month on the forest park until there is significant investment and progress in halting kauri dieback.
