DoC has built nearly all of the 14km first stage of the trail under a certificate of compliance but, after inspecting flood damage to the track, council officers this month ordered a retrospective resource consent.
The Rotorua District Council has not received the application, and could not determine whether the consent application will be open to submissions.
Last week, ratepayers' association members showed the Herald damaged sections of the track to highlight their concerns.
At a bushy cove known as Twin Creeks, a footbridge appears to have been washed away by floodwater and parts of the trail have slipped away to the lakeshore below.
Association chairman Dean Williams pointed out a tree-covered area carpeted in mud and silt.
"I used to call this place the fairy cathedral and I took lots of children and overseas visitors here. Now it's just an ugly hole."
A few minutes' walk down the trail, a steeply sloping, zig zag track built under a cliff face has been nearly obliterated by bad weather.
Extensive timber shoring has failed to retain mud, sand and huge rocks which have pushed large posts sideways and swept away a chunk of track.
"It's not possible to build a safe public trail through this area," Mr Williams said.
Further around, on a hillside facing the lookout of the Buried Village tourist attraction, a landslip has swept a long length of track towards the Te Wairoa Stream below.
"A further concern is that there has now been considerable silt spilling into at least three important trout spawning streams, as we predicted," Mr Williams said.
He said the association wanted the trail built in high ridges around the lake rather than near the water's edge.
"If [DoC] is allowed to continue, another Cave Creek is just a matter of time. The whole idea should now be stopped and no more money wasted. If they have spare money, send it to Christchurch."
DoC Rotorua Lakes area manager Nicki Douglas said the weather had caused "some issues".
"The track will be built to useable and safety standards as required by the district and regional councils, and it won't be open to the public until those things have been taken into consideration.
"There is a safety issue where the slips are, but not to the extent of the whole track. It's a current issue but it won't be an ongoing issue in terms of safety.
"Apart from a few who are appealing against the process, the key message from our partners and the community is, 'Let's get it built so we can get out there and enjoy it'."
