An MPI spokeswoman said final costs often varied from initial estimates.
"The indicative estimate for the refurbishment was in the $100,000-$250,000 bracket and was based on initial scoping of building costs only. Architecture and furniture costs were not included in this tender process," she said.
Even with those architecture and furniture costs of $101,480 excluded, the project ended up costing $51,905 more than the highest estimate - and $201,905 above the lowest.
MPI has faced major biosecurity challenges in the past 12 months, especially with the 1080 infant formula blackmail threat, and the fruit fly emergency in Auckland.
The refurbishment was ordered and the tender awarded months before either of these crises.
The ministry said it established an intelligence, planning and co-ordination group, known as IPC, last year.
To get the IPC group up and running, The Terrace building's level 11 was given a do-up to accommodate necessary staff, meet security needs and provide space for bosses to hold important daily briefings.
According to MPI chief financial officer Thor Gudjonsson, the briefings were "a critical component" in information-sharing about issues crucial to biosecurity, food safety, primary production and trade systems.
NZME News Service asked to see the floor, but the ministry declined, citing "strict security considerations".
MPI said the "small area" known as the raised floor cost $19,830.
Labour Party primary industries spokesman Damien O'Connor said MPI had an important job to do but the renovation resulted in an unacceptable cost blowout.
"I don't think anyone would deny the need for more for an intelligence unit within MPI.
True to form, MPI ... is clearly satisfied with lavish spending on its own premises and operations, yet continues to point the finger at other sectors of the economy telling them all they have to be more efficient."
Mr O'Connor said the spending figures emerged just as dairy farmers were being told to tighten their belts as dairy prices plummeted.
"Every dairy farmer in the country would be interested to know what's been spent on MPI when they are being expected to live on half the income and support the economy," he said. "It's not leading by example, that's for sure."
A Federated Farmers spokesman he'd suspend making judgment on any "extravagance" but biosecurity and food security were important issues.
"Our direct experience during the 1080 scare was that facilities within MPI, physical facilities, were inadequate on occasion."
HEY, BIG SPENDER
The Ministry for Primary Industries isn't the only Government agency to come under fire for its office refit expenses. Last month, the Ministry of Business, Innovation and Employment was derided for extravagant spending at its Wellington headquarters, including:
• $400 on hair straighteners
• $70,000 on a stone sign, including lighting, outside the building
• $140,000 on a television screen
• $260,000 on a sun deck
