A clause in the draft Mt Aspiring National Park management plan opposing any new roads in the park is a "hurdle" for the proposed $160 million tunnel linking Queenstown to Milford Sound.
Southland Conservancy community relations manager Martin Kessick said Milford Dart Ltd had "some issues to address".
Mr Kessick said despite the draft plan's opposition, the department could still consider the application and the Conservation Minister had discretion to grant the concession.
"It's a hurdle the applicant needs to overcome, but it's not a barrier," he said.
An interim decision by the Department of Conservation in November recommended the plan be amended to change the boundaries of the front country zone at the end of the Routeburn Rd to include the area where the Milford Dart tunnel access road was proposed.
However, the final draft Mt Aspiring National Park management plan did not not move the boundary, leaving the location of the access road and tunnel portal as proposed by Milford Dart Ltd outside the front country zone.
The plan now says "the only zone where a new road may be considered would be in the front country zone".
The single-lane 10.2km tunnel, which would run between the Routeburn and Hollyford valleys under two national parks, would cut the driving time to Milford Sound by 55% and create 300 jobs during construction.
Milford Dart Ltd applied to the Southland Conservancy for a concession to build the 300m access road from the Routeburn Rd to the tunnel entrance in 2005.
Mr Stewart said the minister would need to take the provisions of existing management plans, potential environmental effects and whether any adverse effects could be mitigated into account before making a decision.
"The applicant will have addressed the plan provisions in their application.
"They will have provided reasons why the tunnel is consistent with the plans," he said.
A draft report would be finalised by mid-April and sent to the Southland and Otago conservation boards for input.
The department's formal response would then be provided to the applicant.
Milford Dart Ltd will have a chance to respond before a "decision maker" makes a recommendation to the Minister to either grant or decline the application.
If the recommendation was to grant the concession, the application would be publicly notified and the public would have a chance to make submissions.
Following a hearing, the Minister would make a final decision.
Milford Dart director Tom Elworthy said he was surprised the draft plan did not move the front country zone boundary.
However, he was optimistic the concession application would succeed.
The Milford Dart Tunnel would reduce carbon emissions and improve the experience of visiting Milford Sound for tourists.
"The world is changing.
"The current route is an issue and something has to happen," he said.
If approved, the tunnel would be open in four years.
The concession process should be finalised by the end of this year.
The resource consent process would take at most another year and construction would take two years, he said.
The project would cost up to $160 million.
