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But Cure Kids, which raises money for research into child illnesses through Red Nose Day in New Zealand, vowed to appeal the decision and said the fundraising campaign would go ahead as normal this year.
"We have owned the rights to Red Nose Day in New Zealand since 1989, and we continue to do so," Cure Kids chief executive Vicki Lee said.
"The Australians can do their own thing, in their own country. Prior to this challenge that is exactly what has always happened. We will appeal it to the High Court.
"From my point of view, the public don't want to see two charities arguing. It doesn't look good for either charity but we feel that we have to defend our New Zealand rights to this. And we will defend it."
Operating under the name SIDS and Kids, the National SIDS Council of Australia - which funds research and support for families of sudden infant death syndrome - applied to have the New Zealand trademark revoked in 2010, when Cure Kids brought back its Red Nose Day appeal after a 13-year hiatus.
In a decision this month, the Intellectual Property Office of New Zealand (IPONZ) found in favour of SIDS and Kids because of Cure Kids' "non-use" in the three years before 2010.
Ms Lee said the motive of the Australian charity was unclear.
SIDS and Kids chief executive Leanne Raven would not respond to questions from the Herald yesterday.
SIDS and Kids succeeded in its revocation application as Cure Kids didn't run the Red Nose event between 1997 and 2010. The final three years of that "non-use" period are at the heart of the IPONZ decision.
"We've run it all these years before, we've put it on hold, we've brought it back," said Ms Lee. "It's disappointing and frustrating ... "
Last year, the Red Nose Day to Cure Kids appeal - which culminates in a televised comedy event each year - raised $1.6 million.
In recent years, Red Nose Day has featured appearances from Kiwi stars such as Sonny Bill Williams, Jono and Ben, and Flight of the Conchords.
Cure Kids funds research into the treatment and cure of diseases affecting children.
The appeal was important in funding treatments for sick children, said the mother of 10-year-old Cure Kids ambassador Jorja Sharp, who suffered burns as a child.
Louise Sharp said Red Nose Day helped raise awareness and money for research into children's illnesses.
"It's a huge contribution that the public are aware of, for fundraising.
"It's visible for every mum and dad on the street, as well as the corporates."
SIDS and Kids held its first Red Nose Day in Australia in 1988.
Cure Kids held its first Red Nose Day in New Zealand in 1989.
Between 1997 and 2010, Cure Kids did not run a Red Nose appeal.
In 2010, SIDS and Kids applied to the Intellectual Property Office of New Zealand (IPONZ) to have Cure Kids' trademark rights revoked.
IPONZ found in SIDS and Kids' favour this month.
Cure Kids says it will appeal the decision to the High Court.