Meetings between the schools and the ministry have been chaired by independent consultant Janet Kelly.
One of her reports to the ministry, released under the Official Information Act, estimated more than $300,000 a year was being spent by Dunedin secondary schools on marketing, and some schools alleged other schools were using "unethical practices" and "aggressive marketing" to keep their rolls healthy.
One Dunedin secondary school principal, who declined to be named, told the Otago Daily Times their school's marketing budget was about $30,000 to $40,000 a year, and believed it was not the highest in the city.
Another Dunedin secondary principal said they believed $300,000 could be much better spent in the classroom than on marketing.
Ms Kelly's report said a number of schools felt they needed to spend far more on marketing than they wanted, in order to promote success and avoid closure.
Concern was also voiced about the use of scholarships provided by some state schools to effectively buy talented sports pupils for their school; some schools were using the situation to filter the pupils they wanted to attract; and many felt the exorbitant marketing ploys and competition across schools was negatively affecting international fee-paying pupils and relationships between school leaders, Ms Kelly said.
"There was a universal feeling among the majority of state schools that Dunedin secondary schools have traditionally worked in very collaborative ways, which have been beneficial to all schools."
"However, there has been a change to this situation and the current feeling is that this is negatively impacting on students."
Ms Kelly said the relationship between state integrated schools and state schools, in particular, had become uneasy for some.
"The state integrated schools feel the special character of the schools [e.g. religion] should be highlighted and celebrated and do not generally feel that increasing their roll impacts negatively on state schools. They feel that the ministry unfairly targets them to cap growth.
"Some state integrated schools would like to look at maximum roll growth through the differentiation of boarding students versus day students.
"State secondary schools do not share the opinion that roll growth in state integrated schools has no impact on their rolls."
Ms Kelly said the "market-driven environment" of Tomorrow's Schools was seen as creating extra pressures and a disincentive to collaboration.
"Marketing campaigns have hurt other schools.
"Several commented that the business model has a business watchdog to prevent businesses getting too big, whereas education doesn't have this. Maybe the ministry needs to own this."
She said some felt it would take an "ideological change" to get schools working more collaboratively to come up with a strategic way forward for managing the network.
Many schools wanted to get back to the protocols for advertising that had previously been agreed.
"They would like to see things get back to a level playing field.
"It was suggested there be a moratorium on marketing outside an agreed timeframe."
The Ministry of Education has said it would continue sharing information with schools as discussions continued.
Ministry sector enablement and support deputy secretary Katrina Casey said once the report was completed, the ministry would discuss it further with school leaders, before taking action.