Schools are illegally refusing to enrol children by saying their classrooms are too full or insisting on permanent addresses for families in emergency housing.
Attendance services and the legal help organisation YouthLaw said the problem was increasing, and one school was trying to insist that children live in its zone for a year before they could enrol.
The Education Ministry said schools must enrol children who lived in their enrolment zones without delay.
Karyl Puklowski from Auckland City Education Services, which works with children who are not enrolled or absent from school, said some schools were trying to refuse enrolments from homeless children who had been missing school.
One of the main barriers was for families who had been placed in temporary housing, such motels or lodges, due to lack of housing.
"It becomes hard because schools will say that they need a permanent address and they don't view that as a permanent address."
Ms Puklowski said schools would also say they were too full to enrol children even if they were living inside their enrolment zone, and one school was insisting that families live in-zone for at least a year before they could enrol.
She said attendance officers could usually talk schools round, but the schools should be better informed about their obligations.
"Schools do need to be aware that legally they're responsible for the young person to be enrolled if they're in zone for that school, that this is the address that this young person has got at this temporary time and that's all there is to it," Ms Puklowski said.
"It might mean they might be at this school for six weeks and then they have to go to another school, but in the meantime for six weeks they're getting learning."
Jono Campbell from Te Ora Hou Trust said schools in Canterbury and the northern half of the South Island also tried to refuse to enrol homeless children with a history of truancy.
"One of the most obvious situations that comes up is many of the young people are in families who have to go into refuge or escape from domestic violence, abusive relationships, they have no fixed address, so how do you get them into a school," he said.
Mr Campbell said some schools in the area were not pulling their weight when it came to helping to get children back on track.
The principal of Papatoetoe High School, Vaughan Couillault, said several families had approached the school this year after being refused enrolment by their local schools and as far as he was aware, none were in temporary housing or had problems with truancy.
"I get students come to me to say 'I can't go to the school that I'm in zone for because they've shut the doors, won't let me in, said they're not accepting any more enrolments'," he said.
"That's where you would recommend to that family to seek support and assistance from their local ministry office."
Mr Couillault said his school had enrolled some of the students, but in other cases he had directly contacted the principal of their local school or directed their family to the Auckland Ministry of Education office.
"In each case I'm fairly confident the student has got into school, whatever school that may be, but it just seems to me an unnecessary delay to their education," he said.
Mr Couillault said he was not sure why principals would be breaking the rules and refusing to enrol students.
"It could be that some are unaware of what their powers are for want of a better phrase, it could be that some are using that as way of re-engaging with the ministry on issues that are unresolved."
The general manager of YouthLaw, Jennifer Braithwaite, said it had seen a slight increase in cases of schools refusing enrolments because they were at capacity, and particularly popular schools might refuse to recognise temporary addresses.
The Education Ministry's deputy secretary sector enablement and support, Katrina Casey, said children were entitled to enrol in a school if their normal place of residence was within its zone, regardless of whether year levels were 'full'.
"There is also no minimum period of residence required in a zone before a student can attend the local school - any student who moves into the zone has the right to immediate enrolment," Ms Casey said.
"There are scenarios where this isn't clear cut - for example where the address given isn't a student's 'normal place of residence'. We expect schools to consider any such circumstances when they assess enrolment applications, and we can provide advice and support where needed."
Ms Casey said the ministry was not aware of any Auckland schools refusing enrolments because they were full or because students' addresses were temporary.