They found 14 tracks that were not clearly either open or closed, and had no signage or fencing.
Further, they found 20 of the 30 officially open tracks that did not comply with the standards of the CAN.
The majority of open tracks had no signage, no cleaning station at all or a very old one, and in many cases the track surfaces had exposed soil and roots.
The audit also found that fences were poorly placed, so that they were easy to bypass.
In some cases, informal tracks had been made to avoid them, suggesting some people were deliberately flouting the restrictions.
The group called on Auckland Council to urgently close the gaps and tighten enforcement before the summer holiday season began.
"The majority of law-abiding citizens are giving up their beloved Waitakere Ranges tramping experiences in order to protect our forest," Tree Council secretary Dr Mels Barton said.
"We expect Auckland Council to do their bit to ensure that the closure is complete and effectively enforced."
However, council regional parks manager Rachel Kelleher said the audit appeared to have covered a broader area than the CAN actually applied to, which could explain why there was no signage on some of the tracks surveyed.
In other cases, the council was aware that signs could go missing, she said.
Kelleher said the general issue facing kauri in the park was complex and without precedent in New Zealand.
"As with any large-scale closure, we have challenges to work through and we're taking an adaptive approach and continue to learn as we go."
The park had about 90 formal entry points and nearly 200 tracks, which she said presented a range of challenges.
"Our team has been working incredibly hard on progressing protection measures and our programme has expanded since the introduction of the $100 million natural environment targeted rate in July," she said.
"We are at the beginning of a 10-year journey for this investment, and in the last four months have progressed some significant work including track upgrades, new hygiene stations, signage, physical barriers, video monitoring and compliance officers."
While the council's compliance focus had so far been on educating people about their obligations as visitors, it would be taking a stronger stance as summer approached.
"We'll be ramping up our work over the summer months with an increased team of 20 ambassadors working alongside our compliance officers and boosting our communications to ensure that Aucklanders are know what to do."