Cooper was acting chairman after Andrew Rooney moved to Wellington last year.
After the union's annual meeting last month, when Rooney officially stood down and did not seek re-election, a new chairman was sought.
The board - which includes new members, Hamish Walker and Peter McCormack - has met and Cooper has been appointed chairman.
Cooper has been on the board since 2012 when a new constitution brought in more commercial expertise to the board.
The Otago union skirted liquidation at the start of 2012 and managed to survive. A lack of commercial nous was pointed to as one of the reasons the union had got into the red - it had debts of more than $2million - so a new constitution was introduced to appoint directors with more commercial skillsCooper was one of those appointed and had been deputy chairman for the past four years.
He said yesterday the union was in a more positive position then when he first joined the board.
The tough challenges were behind the board but there was still plenty to do on many fronts.
The board had carried out a strategic review last year and that had led to more staff being employed and more resources put into coaching and development.
There were also commercial issues and sponsorship was continually being looked at.
Cooper said sponsorship quite rightly was seen as more than simply a donation these days, and sponsors wanted something back.
The board was also working hard to try to get people along to the games.
The financial focus was about getting in a position where the union could absorb any unexpected hits.
Last year, the union did not get to host a test, costing it more than $100,000 in revenue.
The union racked up a loss of $162,000 last year.
It will host a test this year when Wales plays the All Blacks at Forsyth Barr Stadium on June 25.
Cooper said Otago was in a position where it was not as big as unions such as Canterbury and Auckland, yet it was bigger than other unions in the Mitre 10 Cup.
It had to get to people to matches yet was covering a wide geographic area.
A deputy chairman for the board has yet to be appointed.
