Tensions reached boiling point before, in May, both parties settled a deal, which would see them purchase 28 hectares of land on the eastern face of the peak, close to the existing track and build a new one.
However, in July, the Environmental Defence Society announced it would take the council and the winery to the High Court over the decision-making process which led to the track being cut.
The decision to urgently remove part of the track follows the release of an independent report commissioned by the council and carried out by civil engineering firm Frame Group Limited.
The report said the current state of the Craggy Range track could result in "serious injury or loss of life as a result of retaining wall collapse, falling rocks and slips".
The council's acting chief executive Neil Taylor said the report findings were a "major concern" and urgent works needed to go ahead, to remove any risk to the public.
Taylor said his decision to invoke section 330 of the Resource Management Act (relating to emergency works) was supported by legal advice.
The track was only partially completed and was not formally opened for public use. It has been fenced off for several months due to increased safety concerns.
However, Taylor said some track users have ignored warnings by climbing over the barrier fences, and using the track despite its unsafe condition.
"Trespassers are risking death or injury, and an urgent response is essential."
Craggy Range chief executive Michael Wilding said it was focused on developing an "alternative and superior" track in partnership with Ngati Kahungunu.
Ngati Kahungunu Iwi Incorporated chairman Ngahiwi Tomoana said removing the segment of the track was the "proper thing to do".
"There seems to be a lot more understanding of all the issues now, whereas we were all polarised around our different sets of values before," Tomoana said.
