It has been stripped of its packhouse registration for exporting apples to Taiwan.
MPI central investigations manager Steve Ham said the ministry "takes this sort of offending very seriously".
"Falsifying requests for export certification potentially undermines other apple growers, the wider horticultural industry and New Zealand's reputation as an exporter. Any attempt to circumvent New Zealand plant export programmes is very concerning to MPI. "
Hawke's Bay Chamber of Commerce chief executive Wayne Walford said the company's conduct had the potential to damage the region's reputation.
"It undermines our credibility across horticulture markets and the world. It has the possibility of compromising fruit from Hawke's Bay, which is such a huge component of our economy.
"It would be nice to know they've made a commitment to keep to the rules."
Pipfruit New Zealand CEO Alan Pollard said the company being stripped of its approval to inspect and pass apples from its Ormond Rd, Twyford, packhouse as fit for export to Taiwan, was "a strong mark against them".
"We work very hard to get what are the world's best quality apples into the world's premium markets, and there are certification processes in place, so anything that undermines that integrity is a risk to us."
Hawke's Bay Fruitgrowers' Association president Lesley Wilson said she could not comment specifically on the case, but added: "We have strict standards that the industry must uphold and MPI rigorously audits these standards. We support and have confidence in these audits."
MPI certification provides an official New Zealand Government assurance that export products meet requirements specified by the importing country's government, to ensure plant pests and diseases are not introduced.
Only "Taiwan Suitable" apples can be exported to the Asian island. They must be able to be traced, and have been sprayed to meet specific plant pest spray regimes.
Annual apple exports to Taiwan amount to more than $30 million. New Zealand apple exports amount to $500 million per year in export earnings.
Matipou Orchard Ltd general manager William Thow did not respond to requests for comment from Hawke's Bay Today yesterday.