The changes include a new levy to recover the cost of domestic standard setting and compliance, a further 1c per litre levy on wine exported, and an end to rebates for laboratory testing.
The department says it started subsidising winegrowers' testing to lift exports when the sector was in its "infancy and the costs to be recovered were small", however, the industry is now mature.
New Zealand Winegrowers calculates the proposed changes as costing $2.9 million annually, adding to the annual $200 million it pays the government, via the New Zealand's Customs Service, in excise tax.
"From our perspective, requiring the industry to pay an additional $2.9 million to MPI every year is manifestly unjustifiable," said Steven Green, chairman of NZ Winegrowers. "Other major primary industries are subject to the user-pays regime. However, unlike the wine industry, none of those sectors also pay a product specific tax."
The wine industry had an estimated turnover of $2 billion last financial year, with $1.3 billion of that in export earnings, according to a survey released by Deloitte and New Zealand Winegrowers.
Last year the government collected $892 million in alcohol excise, which it charges the manufacturer in a bid to deter excessive alcohol consumption.