Ministry of Education deputy secretary, regional operations Katrina Casey said "the ministry can direct a school to enrol a student who has been refused enrolment and lives within the enrolment zone of that school.
"However, it only directs a school to enrol a student when all other options have been considered."
Ms Casey said the ministry had worked with the parents and family to help enrol the student in an appropriate learning environment, including a youth training programme.
"Students over the age of 16 who are not enrolled in a school usually find vocational learning programmes that may be provided by alternative training facilities," she said.
Ms Casey said schools and parents or caregivers often worked together to help students get back into school.
"Many excluded students return to a learning environment without the ministry needing to be involved," she said.
Ms Casey encouraged parents or caregivers to contact their local ministry office, youth law representative or Parents Legal Information Line for School Issues (PLINFO) to seek advice about learning options.
Makoura College principal Tom Hullena confirmed the school had declined to enrol the girl but said another option had been presented. "Which, in our view was in the best interests of the school and the girl".
Under the Education Act 1989, the board of a state school may refuse to enrol a student, who is for the time being excluded or expelled from another state school.
According to PLINFO the Secretary of Education can lift the exclusion or direct the school to enrol the student.
The parents have permanent name suppression to protect the girl's identity.