The Fiordland Experience proposal cut through the conservation estate, but Dr Smith said it was significantly different from the tunnel project because "very little" of it was within Mt Aspiring or Fiordland national parks.
A section of the monorail track would run through areas of special grassland and spots that contained endangered kaka and yellowhead - two factors which were influential to its Outstanding Universal Value.
Unesco has warned the Department of Conservation that the development was "likely to be considered incompatible" with the site's World Heritage status. But Dr Smith believed that this suggestion was "overcooked" because many of the 200 World Heritage spots around the world had visitor facilities which were similar to the proposal.
Fiordland Experience said it was more optimistic after yesterday's announcement because the competition for a bypass had been reduced.
It predicted 20,000 more visitors a year to the region if a new route was created to half the 4-hour travel time from Queenstown to Milford Sound.
A hearing commissioner is expected to produce a report on the monorail project for the minister this year.
Dr Smith's decision on the tunnel came after meeting Milford Dart Ltd, consideration of a report based on 1260 public submissions and advice from the Conservation Authority.
But his visit to the site this year also had a profound impact.
"When I thought about half a million tonnes of tunnel spoil being dumped into the ... pristine environment of the Hollyford Valley, I took a deep breath ..."
He had also been concerned that one of the tunnel's entrances was too close to one of the country's Great Walks, the Routeburn Track, and that the company had underestimated the cost of making the tunnel safe.
Stop the Tunnel spokeswoman Leslie Van Gelder said his decision was a "totally unexpected" result.
"The quiet, the beauty, the way you arrive at the Routeburn would have all been destroyed - the wildlife would have been gone."
Milford Dart had no comment to make yesterday.
The company had last week proposed an alternative, longer tunnel which removed one entrance away from the Routeburn Track, but Dr Smith said it was too early to respond to the new plan.
The minister said it was highly likely that his decision would be challenged in court, but he was confident that it was robust.