The ministry was formed as a result of the completed merger of the MAF with Ministry of Fisheries and the New Zealand Food Safety Authority during the first term of the National-led Government in 2008.
In a statement, Primary Industries Minister David Carter said the new name reflects the range of government work the ministry carries out, including horticulture, aquaculture and biosecurity.
He added that there had been strong support from primary industry groups for the name change.
The ministry had been known as MAF since the 1970s, prior to which it was known as the Department of Agriculture.
The new name takes effect on April 30 2012.