It said Ghuznee St was also closed between The Terrace and Victoria St.
Motorists should avoid the area if possible, and people travelling to the airport should allow themselves more time.
Wellington Water chief wastewater advisor Steve Hutchison said it was not yet known how the break happened or how long it would take to fix.
Staff will be working shifts to put in temporary fix and after that they would start on a permanent solution.
"We're working on three fronts at the moment to clear an old decommissioned pipeline to get the wastewater flow up back up and flowing through that as a temporary diversion," Hutchison said.
"And also looking at ways we can get the flows in this catchment ... across to neighbouring catchments to get the flow back to Moa Point and get it treated."
In the meantime he said wastewater and sewage - up to five million litres per day - could keep pouring into the harbour for days.
Hutchison said people should stay out of the water in the inner harbour - from the top of Roseneath through the waterfront to the port - for now while testing was done to determine how far the contamination has spread.
However, local iwi have placed a rāhui on the entire Wellington harbour.
Kura Moeahu of Te Atiawa said the rāhui was a commonsense precaution to keep the public safe.
Wellington Water chief executive Colin Crampton said it couldn't have come at a worse time, when lots of people were wanting to swim in the harbour.
He said he apologises to Wellington residents and visitors and they were working as hard as they could to fix the problem.
In the meantime Crampton is asking people downtown conserve water, which will help ease the flow into the harbour.
He told Nine to Noon it was a very tricky situation because the collapse was deep underground.
The discharge points are near the dive platform and Whairepo lagoon on the Wellington waterfront.
- RNZ
