While AT "appreciated that this was frustrating for cyclists", Nelson said engineers made an assessment that the tunnel needed to be closed to keep cyclists safe.
However, as the damage was more than 5m from any traffic lanes it was fine to keep the road open to traffic.
Detours were put in place about 3am, with hand-written signs alerting cyclists.
The signage, which Nelson said was "quickly put together", and the managing of the detour frustrated some.
Taking to social media, Ben Gracewood said: "The fact that there weren't at least stop-go people on the road and cycleway this morning is a complete dereliction of safety culture."
He said bent rebar, and sunlight could be seen coming through the hole left by the damage.
Nelson said: "We are working with Fulton Hogan to ensure that signage for the detour is improved so that it is clear to cycleway users where they need to travel in order to safely continue their journey."
People will also be on-site this afternoon between 2.30pm and 6pm to help cyclists and pedestrians navigate the detour, he said.
AT and Waka Kotahi were working with Fulton Hogan today to figure out the scale of the damage and what would be needed to repair it.
Nelson said: "Our top priority is ensuring the safety of people using the Northwestern Cycleway, so we will not be reopening the underpass until we are confident it is safe for use by cyclists and pedestrians.
"This underpass is a vital section of the Northwestern Cycleway, and it is important for it to be repaired and made safe for use as soon as possible," he said.
