Under the programme, workers support schools and whānau when children experience wellbeing issues such as bullying, parental separation, grief and loss.
Rotorua Intermediate principal Garry de Thierry believed students were "missing out on other resources" because the school employed a qualified counsellor and two other full-time support staff using its operational fund.
The staff were supporting between 60 and 70 students on an ongoing basis. The school's roll was about 730.
The school has spent more than $1.5 million of its operational expenditure on counsellors in the past 15 years.
"I think it is wrong. That money could be resourcing a whole range of other things within a school," he said.
But he said the staff were crucial in dealing with a "huge" range of issues presenting in intermediate-aged students.
"It is a real wake-up call for the Ministry of Education to start appreciating complexities and challenges that a lot of students are facing – and putting that support in really early.
"Teachers don't have the time to sit down and unpack what is going on, and to work out where support is needed."
He said students could self-refer to the service, and families were included in counselling sessions on a "case-by-case" basis.
De Thierry said it was important not to blame students experiencing mental health problems.
"Behaviour is just a reflection of what is going on in their life. Most issues are happening outside of the school environment."
Rotorua Principals Association president Gary Veysi believed Covid-19 had amplified mental wellbeing issues that already existed.
He had seen demand for mental health support increase since starting work as a principal 20 years ago.
"We are really trying to address the problem. There is a whole new level of issues tamariki are facing," he said.
At Mamaku School, where Veysi was principal, a social worker provided part-time wellbeing support to students and families.
Asked if the school was meeting the demand for this type of support, Veysi said: "We are just keeping our head above water."
But he said the problems they were dealing with might only be "the tip of the iceberg".
Mount Maunganui Intermediate School lost student Blake Dalley to suspected suicide in December.
Mount Maunganui Intermediate principal Melissa Nelson said the death was a "tragedy" that hit the school community "hard".
She said Blake's death proved the need for Government-funded counselling at intermediate schools.
The school was able to access $18,000 of emergency funding through the Ministry of Education after Blake's death, employing two part-time counsellors.
It continued to fund the positions from its operational funding.
But this money would not be available next year.
The counsellors were working with about 50 students. Another 30 students had previously been working with the counsellors, and 14 were on the waitlist.
"Being able to refer a struggling young person to an expert on site has been a huge help to us and to their families."
Nelson said the number of students presenting mental health issues weekly was "staggering and incredibly worrying".
"Secondary schools do have a staffing allocation for counselling staff, which tells me that the Government thinks that 12- to 13-year-olds do not have the problems or need the same level of support that secondary students require.
"My staff have had to deal with a worrying number of young people with serious mental health worries."
This had put "immense" pressure on staff and taken a toll on "already hardworking" teachers.
She expected her school was not the only intermediate in the country experiencing "such frustration" at the lack of resources to address mental health among students.
A fundraising event had been organised to raise money to continue the school's counselling service next year.
Ministry of Education operations and integration leader Sean Teddy said schools were "free to use" their operations grants to best meet their needs, including employing counsellors.
Progress had also been made on the extension of Mana Ake in the Bay of Plenty, led by local DHBs, with schools and iwi.
A Health Ministry spokesperson said it was aiming to tailor the programme design to the specific needs of the local schools.
Decisions regarding the future rollout and funding would be made once the co-design report had been presented and considered, the spokesperson said.
In April it was announced Mana Ake would expand to five new DHB areas - including Bay of Plenty and Lakes.
An event has been organised to help raise money for a Mount Maunganui Intermediate counselling service in 2022. The masquerade casino event will be held at Classic Flyers on March 11.
WHERE TO GET HELP
• Lifeline: 0800 543 354 (available 24/7) • Suicide Crisis Helpline: 0508 828 865 (0508 TAUTOKO) (available 24/7) • Youth services: (06) 3555 906 • Youthline: 0800 376 633 • Kidsline: 0800 543 754 (available 24/7) • Whatsup: 0800 942 8787 (1pm to 11pm) • Depression helpline: 0800 111 757 (available 24/7) • Rainbow Youth: (09) 376 4155 • Helpline: 1737 If it is an emergency and you feel like you or someone else is at risk, call 111