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Clinton parents Donna Davey and Shane Dryden, who now live apart, appeared last week in the Dunedin District Court, where they each admitted a charge under the Education Act of failing to ensure their child was enrolled.
Counsel Jo Turner said the parents were "at a loss" to know what to do with their slothful teen.
"[They] have tried everything they can to get him out of bed," she said.
"He refuses to get up in the morning."
The Ministry of Education was asked whether a $50 fine would deter other parents, but deputy secretary of sector enablement and support Katrina Casey said it was inappropriate to comment on the decision of the court.
The boy, who lived with Ms Davey, was enrolled at Clinton Primary School until the end of 2017, then at South Otago High School up to May this year.
However, the court heard, during those periods he was unenrolled at various times because of the sustained spells of nonattendance.
At one point in 2018, the teenager had racked up 38 days of unjustified absence and seven days of justified absence out of 62 school days - off school nearly three-quarters of the time.
With every 20 days of unjustified leave, the boy was removed from the school roll.
The final occurrence was in May, when the Ministry of Education sent his parents a letter threatening criminal charges.
A month later and there was no change. The teen remained unenrolled.
"Considerable effort has been made by various state agencies to ensure that the defendants enrol [their son] at school and have him attend school regularly," a summary of facts said.
Community Magistrate Simon Heale accepted the parents had made some effort to get their child to school.
"I understand teenagers can be very difficult to coax into compliance," he said.
"But it is your obligation, till he reaches the age of 16, to have him at school."
The ministry said the prosecution was the first since 2017 and the fourth since 2014.
"While prosecution for non-enrolment is available, prosecuting parents is absolutely a last resort," Ms Casey said.
It was both Davey's and Dryden's first appearance before the court.
Along with the fine, they were each ordered to pay court costs of $130.