Work to manoeuvre the pipe through a 1.6km drilled hole under Tauranga Harbour - the riskiest part of the $21 million crossing - began last Friday.
Most of the distance was covered in the first few days but crews ran into issues with the final 40m on Tuesday last week.
The 900mm-wide pipe was not lining up with a steel sleeve installed to take it through the softest ground.
Thomas said contracting teams spent days trialling different ways to get the 1500 tonne pipe to just the right level of buoyancy to move through the sleeve, but nothing was working.
On Friday a workable plan was finalised to pump air into the pipe, and 24 hours later it was through.
"There was a palpable sense of relief," Thomas said.
"Now that it's through we can relax a bit. A lot of the risks have been managed or gone away, for example, the hole collapsing."
It was a key milestone for the $99 million project, which has been plagued by delays and complications that have put it years behind schedule since it began in Greerton in mid-2010.
The pipeline will move wastewater to the Te Maunga wastewater treatment plant, taking pressure off the Chapel St treatment plant.
Thomas said that over the next few weeks the black plastic pipes that will eventually contain the wastewater will be welded together, tested and threaded through the outer pipe.
The entire project was likely to be finished by mid-October.
