Commerce minister Craig Foss said implementing the system here will give "a significant boost" to New Zealand entrepreneurs and exporters selling and marketing products overseas.
He congratulated avocado exporter AVANZA and outdoor clothing manufacturer Betacraft for being two of the first kiwi companies to file applications.
"These companies have clear export growth potential. With the Madrid Protocol, it is now easier for them to register their brands in up to 87 countries and protect their trade mark as they expand into more markets."
IPONZ also this week launched its overhauled online system for applying for and managing patents.
"The online system cuts down on processing times, removes the need for paper filing, and reduces compliance burdens," Foss said.
By joining the Madrid Protocol, New Zealand brings itself into line with major trading partners such as Australia and the United States, which signed up in 2001 and 2003 respectively.
The Madrid Protocol is administered by the International Bureau of the World Intellectual Property Organization (WIPO) in Geneva.