RNZ obtained an email sent to Ministry of Education officials by a Ka Ora, Ka Ako nutritionist after they visited some Auckland schools and saw the meals delivered first-hand.
In the email, the nutritionist said they were "hoping service was rolling better".
"Unfortunately that was not the case," the email said.
They then listed a host of issues, including:
• An estimated 50 percent surplus of unopened lunches
• Serious menu fatigue
• Concern over quality and choice
• Out of control waste - with schools having to cover land fill costs
• Deputy principals spending hours in the kitchen and distributing the school lunches
• Major concerns over halal safety
• Difficulties contacting the School Lunch Collective
The Ministry of Education declined to be interviewed about the school lunch programme.
But professor of population nutrition and global health at University of Auckland, Boyd Swinburn, told RNZ they were trying to compare the new system to the old one.
"We are trying to analyse the quality of the lunches compared to an analysis done under the original system, but we need quite a bit more data from the providers to do that.
"Just on a first look, it seems very clear that one of the things they have done is to chop back on the size and the calorie content of the lunches quite considerably - probably chopping them back by a third at least - so that's probably where some of their cost savings are."
He said the kids were getting about 11 or 12 percent of their total energy needs for the day in the lunches that are served under the programme.
Swinburn said the old lunch provided was "about twice that, about 20 percent."
He said there were 88 complaints about the menu appeal and 200 about the quality over the three years the old school lunch system ran.
"We've had that number of complaints in the first week just about, so there is definitely unhappiness across many of the schools."
He also said all calories were not always equal and there were requirements.
"There are different criteria for vegetable requirements and protein requirements in the meals, and we don't know if they are being met or not.
"We need the recipes from the providers to be able to analyse that, we need to know what the requirements in the contract are - are they expected to stick to the original nutrition criteria, we don't know, there's a heck of a lot of questions on this."
He said they had asked for the contracts and will soon be asking for the nutritional break-downs.
"It's clear from what we do know that the lunch is a pale comparison compared to what has been available before."
He said year nine's and over were receiving 378 grams in a lunch, but that had gone down to 300 grams, while years 4 - 8 were previously getting 300 grams but were now down to 240 grams.
He also said there was a serious waste problem and the school staff were spending hours in the kitchen helping to distribute the lunches.
"Apparently schools are not being well compensated for that, so there is a lot of extra time the schools are having to pick up to make this work."
Swinburn said the costs - with the additional snacks - were unto $3.84 a pop.
The Ministry of Education sent Checkpoint a response from Sean Teddy, the leader of operations and integration.
It said the nutritional standards had not changed and were the same for all providers in the Ka Ora, Ka Ako School Lunches Programme.
Teddy said the nutritional standards were the minimum weight of food for students and that these had been informed by the Ministry of Health's Healthy Food and Drink Guidance.
He said the minimum size and weight of the school lunch meals had not changed with the introduction of the new programme, apart from Year 0-3 who were receiving a slightly larger meal.
RNZ invited the School Lunch Collective, which was responsible for the revamped school lunches regime, to speak but - as has been the case since the start of the year - they declined.
