A council spokeswoman said some boundaries along Havelock Rd had encroached on to public land and, to build the cycleway, fences had to be moved and greenery removed.
"The costs of the physical works to re-establish the legal boundaries are being covered by council and, where required, owners have been compensated for things like the loss of plants," she said.
"Council has received a complaint from one resident on the opposite side of the road, who was worried there had not been enough consultation with affected owners.
"However, council was able to confirm with her that the owners are happy and had signed an agreement with council."
Resident Malcolm Frost said he was concerned about increased traffic noise with the loss of large trees and bushes but overall it was a "win-win".
Councillor Wayne Bradshaw, a critic of hazardous bollards on the completed cycleway on the opposite side of the road, said the finished project would look "very nice".
He said his personal view was because central government was paying more than 60 per cent of the project it was a good opportunity to widen public access for the second-busiest road in the district, behind Omahu Rd.
A totara hedge near St Georges Rd would be replaced with a planted bank.
"It is sad to take some of the older trees but sometimes you have to reset the clock," he said. "The legal boundary is the legal boundary."