Many protesters were visibly upset that their efforts had failed.
Mr Edwards said he was sad that the trees had gone and felt there was no business case to remove them, given the traffic numbers along SH1 through the city had decreased by about 800,000 a year.
NZTA regional director for Northland/Auckland Stephen Towns said the extra security contingent was needed to ensure work proceeded.
"Our plan was to start [cutting the trees down] Saturday morning, but a small number of protesters got into the park and in the trees."
Mr Towns said NZTA went though due process in obtaining consent for the work and while traffic counts had gone down on SH1 in recent years, that had happened throughout the country during the recession.
"It's future-proofing. If we did cut back the project to a future date people will complain in five years time that we did not do an adequate job."
But for Hone Shortland, who helped organise the protests, there was no valid excuse to justify cutting down the trees.
"The trees are going, but people can be proud that they made their feelings known," Mr Shortland said.
"We've had thousands of people tooting support for us as they've driven past on SH1, but the council and NZTA have ignored all their voices."