The Otago board's annual report for the year which ended in June shows Mr Rousseau's salary at between $460,000 and $470,000.
But although this was an increase of about $90,000 from the previous year, when his remuneration was between $370,000 and $380,000, the cost to the Otago board was slightly less last year because of Mr Rousseau's dual role.
Otago paid $360,000 to $370,000 last year with the Southland board, which has had Mr Rousseau acting as chief executive since October 2007, picking up the remaining amount of about $100,000.
In October this year, Mr Rousseau was permanently appointed to the Southland position, and has had a salary review since.
Otago board chairman Richard Thomson said this week Mr Rousseau's salary was now set and, while he could not say what it was, it had gone up "a little bit" but had not really changed very much.
Mr Thomson also explained that Mr Rousseau was the Otago board's employee.
The board had a contract with its Southland counterpart for Mr Rousseau to provide chief executive duties for the Southland board.
That arrangement was necessary to solve quite complex employment issues surrounding the dual role and a memorandum of understanding between the boards outlined how it would work.
Mr Rousseau was one of 12 of the senior executive team who had a portion of their pay designated "at risk", with them being required to meet specific goals before it was paid out.
Last year, 11 payments were made, with one payment between $40,000 and $49,999, the parliamentary health select committee was told earlier this year.
Several executive salaries are split between the boards on a population basis, with Southland picking up a total of $201,015 of the cost last year.
The annual report shows the number of people employed by the board who are paid more than $100,000 is up by 18, at 202 (183 of them medical or dental staff).
Projections given to the health select committee indicate the number in this band is likely to rise a further 62 this year.
Last financial year, there were also 94 part-time staff who would be paid $100,000 or more if they were working full-time.
In the 2006-07 financial year, Mr Rousseau was not the highest-paid employee, but he has a clear lead now, with the next highest-paid staff member on $380,000 to $390,000.
While the annual report does not indicate who may be receiving this pay, the health select committee information suggests it is likely to be a clinician.
The projections for this year show that the next highest-earning non-clinical staff member below Mr Rousseau will be in the $260,000 to $270,000 bracket.
Last financial year, a total of 11 staff, type unspecified, had salaries ranging from $300,000 to $390,000 compared with five the previous year.
Termination payments to employees were up last financial year by more than $118,000, with 12 employees receiving payments totalling $261,181.
These ranged from $314 to $70,918.
The previous year there were only four payments, the highest almost $51,000.
The board's total expenditure on staff was $181,178,000, more than $9 million over budget and up by more than $25 million from the previous year's total, despite staff shortages.
Mr Thomson continued to be the highest-paid board member, again receiving $49,000, followed by his deputy Susie Johnstone ($29,000).
The lowest-paid member on $10,000 was Mary Gamble, who left the board last year to go overseas.
