It began work on the proposed plan changes a year ago. However, progress was hampered by the sheer number of trees - about 5400 - which were nominated for addition to schedules of protected notable trees in the former councils' district plans.
A list of 1819 prospects was weeded out by arborists using a standard assessment method. Work was delayed while the council sought a declaration from the Environment Court on whether changes to the Resource Management Act meant each tree in a cluster had to be specifically identified on the plans.
Across Auckland, the district plans were complex and varied and the council had to deal with 18 local boards in getting nominations.
Judge Newhook held that the circumstances were probably unique and the delays were understandable.
The council was the only party in court so the judge appointed Russell Bartlett, as a senior specialist environmental lawyer, to help by raising arguments in the private as well as public interest.
Mr Bartlett said that Parliament had in 2009 considered a "head-start of two years and three months" to be enough time for councils to put in replacement controls. He said the private interests potentially affected by the making of the order were those of property owners and occupiers who would have enjoyed rights in respect of those trees that they did not presently have. Affected land owners could not trim, damage or remove the nominated tree without first getting resource consent and paying an application fee.
Mr Bartlett said Parliament had seen the risk or mischief of landowners acting ahead of a proposed plan change as a lesser mischief than the problems of having to comply with two sets of sometimes contradictory rules while waiting for plan changes.
A council spokesman said the court order covered 829 trees across the region which would have been left without protection on January 1.
The court order also boosted protection for notable trees proposed for scheduling - even where a resource consent was needed under a surviving district plan rule.
Auckland's former councils, except for Franklin District, had extensive general tree protection rules in their operative district plans, before being replaced by Auckland Council in November last year. The Resource Management (Streamlining and Simplifying ) Amendment Act largely revoked district plan rules for general protection of trees in urban areas from January 1, 2012.
Judge Newhook said council witnesses said it would not be possible to process the changes and make decisions on submissions for about another six to nine months. Many of the trees would be at risk of being felled in the absence of the new rules having legal effect.