For the first time, the number of Otago and Southland pupils gaining NCEA level 2 or above reached 3000 in 2015, which equates to 83.2% of school leavers.
Nationally, school leavers with NCEA level 2 increased to 79.1% in 2015.
The ministry is aiming for 85% of school leavers to have NCEA level 2 in 2017.
Otago Secondary Principals' Association secretary Gordon Wilson said Otago's secondary schools were ''well over'' that target already and about 88% of school leavers already achieving NCEA level 2.
''It's a testament to the very solid work being done by schools and all those in schools, and also by the young people themselves.
''Otago statistics continue to be among the highest in the country in all categories.''
The data comes from the Ministry of Education's 2015 Public Achievement Information (PAI) report on NCEA and National Standards, which was released yesterday.
PAI measures the performance of New Zealand's education system - in particular, how many children are in early learning, how children are doing at reading, writing and mathematics, and how many young people are achieving NCEA level 2.
Ministry director of education and former Queen's High School principal Julie Anderson said schools and other education providers were working hard to make sure young people in the southern region had the qualifications they needed to take up further work or study.
''With tools like Vocational Pathways and our support, they are connecting students with industry training organisations and tertiary providers, such as the Otago Polytechnic and the Southern Institute of Technology.''
She said the figures also showed the region had the highest percentages of pupils achieving the standards in reading, writing and mathematics.
Mrs Anderson said every percentage point increase represented hundreds of pupils.
''We're especially pleased to see that schools are tailoring support to individual students, using a range of data and evidence.
''Families and whanau are also getting involved, and contributing to programmes such as Reading Together.
''This helps our kids enjoy the sort of success we all want them to experience at school.
''We won't stop there. Programmes for students such as ''accelerated learning in literacy'' are under way to strengthen achievement in writing, for example.
''Many of our new 'communities of learning' are targeting writing or mathematics, or are exploring ways to support groups such as Pasifika students.''
