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The salary, $390,000 to $399,999 in 2012-13, was released alongside other state sector heads by the State Services Commission.
Southern is the largest of the 20 health boards by land mass, and in 2012-13 had the sixth-highest revenue.
Contacted for comment, board chairman Joe Butterfield said that because it was Ms Heatly's first full financial year in the job, her salary did not include a performance payment from the previous year.
Her pay should not be compared with the heads of MidCentral DHB ($520,000 to $529,999), Canterbury DHB ($530,000 to $539,999), or Bay of Plenty DHB ($480,000 to $489,999), Mr Butterfield said.
''It's comparing apples with oranges, because of the way in which pay is assessed after year-end.''
Ms Heatly started the job in March last year.
University of Otago vice-chancellor Prof Harlene Hayne was Dunedin's highest-paid state sector head, receiving $520,000 to $529,999.
Her pay was lower than the heads of the University of Auckland and Massey University, but equalled Victoria University's, and was higher than the heads of Canterbury and Waikato universities. Otago Polytechnic chief executive Phil Ker had an increase.
His pay was $330,000 to $339,999, compared with $320,000 to $329,999 the previous year.
In Invercargill, Southern Institute of Technology chief executive Penny Simmonds received $270,000 to $279,999, up from $250,000 to $259,999 the previous year.
Aoraki Polytechnic's former chief executive Kay Nelson departed in December last year. She received $170,000 to $179,999 from July to December 21, including final day entitlements of more than $77,000.