In the decision, the panel said the only trees removed from the schedule as a result of their visits to submitters' properties was a group of totara shading a house in Sunnypark Ave.
Council experts said the trees scored 138 points, above the Stem threshold of 126 points for inclusion.
But the owners wanted the option of being able to remove them without going through the long and costly process of getting resource consent.
The panel said: "The trees dominate and overhang much of the house and as a result it receives very little sunlight and is cold and damp.
"Also the trees are dropping considerable amounts of leaf and should any limb fall off it will crash onto the house's roof."
The adverse effects of the trees on the owners and neighbours outweighed the positive community effects.
The commissioners said the Stem method failed to address wellbeing and health and safety of people - one of the purposes of the act.
Greater weight was placed on the value of the tree itself and its contribution to the wider community.
However, the commissioners rejected a bid by Housing New Zealand to stop the scheduling of three totara on the front boundary of a Smiths Ave property.
The corporation complained that scheduling restricted its ability to maintain, alter or redevelop.
The panel said the trees' Stem rating was 136 because of their visual appeal and because they contributed to the amenity of the area without damaging houses.
The council said the Stem method was endorsed by the Royal New Zealand Institute of Horticulture.
As well as an arborist making an inspection, the council reporting planner visited the Sunnypark trees and considered that the installation of roof gutter guards could prevent problems.
The trees did not appear to be a hazard.