University of Otago vice-chancellor Prof David Skegg earned between $460,000 and $469,000 last year - about $130,000, or 39.3%, more than he was paid in his first full year in the job in 2005.
Otago Polytechnic chief executive Phil Ker's salary increase has been less spectacular but it has risen by about $60,000, or 28.5%, since 2005.
Salary increases over the same period have been more modest for other southern tertiary institution chief executives, with Telford Rural Polytechnic's Jonathan Walmisley earning about $40,000 more, Southern Institute of Technology's Penny Simmonds increase about $30,000 and Aoraki Polytechnic head Wendy Smith receiving about $10,000 more.
Tertiary institutions are required to provide the State Services Commission with annual salary band information for their chief executives and non-academic staff.
The information is collated in the commission's annual reports.
The 2008 report listing salary payments for the preceding calendar year was released earlier this month.
Prof Skegg runs New Zealand's second-largest university, with about 20,000 students and more than 3000 equivalent full-time staff.
Its turnover this year is expected to be $447 million.
In the salary stakes, he has risen from fourth highest-paid tertiary executive in the country in 2005 to second-highest last year.
Retaining the top spot in 2007 was University of Auckland vice-chancellor Stuart McCutcheon, who received $520,000 to $529,000.
Massey University vice-chancellor Judith Kinnear, who retired earlier this year, was also in the $520,000 to $529,000 band, although the annual report said some of her total included payments relating to previous periods.
Canterbury University vice-chancellor Roy Sharp received $450,000 to $459,000 last year, while Victoria University of Wellington's head Pat Walsh earned $360,000 to $369,000.
Senior non-academic staff throughout the tertiary sector have also enjoyed significant salary increases since 2005.
Nationally, 1654 managers were paid $100,000 or more in 2005, with 44 of them earning more than $200,000.
Last year, the total earning $100,000-plus had jumped 63.9% to 2640, with 113 people earning more than $200,000.
