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The decision to exclude the Homer Tunnel section of State Highway 94 from the race which previously ran from Milford Sound to Te Anau was to protect competitors from possible rock falls.
The rock fall situation has resulted in road closures by the New Zealand Transport Authority (NZTA) since early December and about 20km has been trimmed from the 120km race distance.
Organisers said they were confident a shortened route would still provide participants with a positive race experience.
Race committee chairman Don McFarlane said safety of competitors was paramount.
''If NZTA believe there is a real risk to participants, then there is no alternative but to move the start to avoid this hazard.
''We are delighted that the event can still go ahead, albeit as 100km instead of 120km, and believe the 100km route will still provide participants with a challenging race through some of the world's most spectacular scenery.''
NZTA Southland area manager Peter Robinson said the decision was likely to disappoint some, but the right one had been made.
''Cyclists would have limited ability to get to safety, even with the safety systems we have in place, and that is a risk we are simply not prepared to take and, while obviously disappointed, the race organisers understand our position.''
The western tunnel entrance and the highway for several hundred metres towards Milford Sound will be transformed into a construction zone by race day.
The race will now start at the Homer Hut car park.