Education Minister Hekia Parata has said those figures are incorrect and comparisons with partnership schools is complex because they are run and funded so differently.
However, Mt Albert Grammar School headmaster Dale Burden said if funding per student worked out to be above the alternative education rate that was frustrating.
His school contracts community providers to deliver alternative education for young people aged 13 to 15 and who have become alienated from the mainstream system.
"The whole partnership school thing seems to have certainly got much better treatment than alternative education has, which is pretty disappointing from my point-of-view."
Another person involved in alternative education, who asked not to be named as the Ministry of Education is effectively their employer, said the two systems had similar aims, but not funding.
A new alternative education provider was recently established with no such grant, for example, whereas a Northland partnership school used government money to buy $600,000 of farmland.
"It's frustrating to see the money being thrown at charter schools when we remain the poor relation, trying to do the same job on a shoestring budget.
"The Government is spending millions to create what we already have ... the alternative education sector could be expanded and funded properly to be able to pay qualified teachers to teach those most in need of a lift."
Ms Parata's office referred questions to the Ministry of Education yesterday. A spokesman said alternative education should only be used as an extension of a school's approach to meet the individual needs of some students.
Labour's education spokesman Chris Hipkins said large amounts of money have been pumped into charter schools.
"When actually there are a whole lot of other programmes like alternative education who are doing a fantastic job and aren't getting that same level of funding, but who are actually genuinely targeting areas of need."
