The board and other trusts were prevented from making such payments when the Trusts Act 2019 came into effect in 2021, unless they obtained court approval.
Otago Museum decided it should pursue it.
Chairman Prof David Hutchinson had in recent years missed out on the traditional annual allocation, despite what the court agreed was a significant workload.
In her judgement, Justice Helen Cull said the board’s application was administrative in nature.
"It involves a narrow issue of whether remuneration for the chairperson in the modest sum of $10,000 per annum is just and reasonable."
She determined it was and that retrospective payments should be approved.
Responsibilities of the person chairing the board included setting the agenda for meetings, participating in staffing committee meetings, representing the board at functions and ensuring the museum met legal obligations, the board submitted.
The museum was described as a "large and complex operation".
"I accept the board’s submission that these services are complex, time-consuming and require specialist knowledge of the Otago Museum’s operations with a governance skill set," the judge said.
Prof Hutchinson stood aside from discussion about the application to the court, but the rest of the board agreed it should be made.
Deputy chairwoman Laura Black said such payments had been a longstanding convention.
Ms Black, who has 35 years’ experience in the not-for-profit sector, said the clause in the Act preventing them seemed too broad.
The Otago Museum Trust Board had taken the view the proposed remuneration would not reflect the full effort of its chairman, but might provide some recognition, Ms Black said.
The board has not yet met since the court’s decision and is set to do so next week.
