"There's a clear correlation between anything below 90 per cent [attendance] and NCEA cumulative results [being] affected seriously," Mr Shepherd said.
"Truancy continues to be a problem. Most schools would have some persistent truants."
Mondays and Fridays were the most common days for absences - when parents would provide "feeble" excuses, he said. "It's what I would call 'condoned truancy'."
Every school had its own programme to deal with absences, but the RockOn programme - a multi-agency approach with local police - was having good results at Kuranui College.
"[Police] will even go to the home and deliver letters for us."
The school would jump on any patterns, such as regular Mondays or Fridays off, and quickly address them, he said.
The attendance survey gathered information from 1950 state and state-integrated schools on student attendance over a week in June last year. The total national absence rate last year was 10.1 per cent, or about 73,500 students each day.
About 17,500 of those students were away from school without justification - a rate similar to that of previous years.
Truancy peaked on Fridays and Mondays, as did "justified absences", the report showed.
Schools are also struggling with "parent-condoned truancy", including parents pulling kids from school to take advantage of cheap overseas holiday deals.
Principal Youth Court Judge Andrew Becroft said not attending school was a "massive risk factor".
"Apart from being male, the single biggest characteristic of young offenders we see in the Youth Court is that they're disengaged from mainstream, and often all, education," he said.
If there was a "magic bullet" to reduce youth offending, it would be keeping all young people involved in school until their 17th birthday, he believed.
The Ministry of Education and schools were making a bigger effort to retain students.
This had contributed to "record low" numbers of young people being apprehended by police and appearing in the Youth Court, Judge Becroft said.
At the beginning of last year, the Government created the Integrated Attendance Service, and an additional $4 million a year was put aside to reduce truancy.
Parents can be prosecuted if their child is away from school without good reason.
- additional reporting Nicholas Jones.