The wage error was picked up by a new staff member called to work late one Friday night in 2011.
She realised her pay was not as much as at her previous job and checked the contract.
"On closer inspection of this clause I believe all evening callouts are being paid incorrectly and any call between the hours of 2000-0800 should be paid at T2 [double time]," she wrote in an email to the payroll administrator.
Some backpay was paid to some staff members before the board revised its view of its obligations under the contract's clause.
The board told the authority that there had been a drafting error in the collective agreement.
"[Staff union] APEX has been accused by the board of trying to take advantage of the alleged mistake," said authority member Alastair Dumbleton.
APEX national secretary Deborah Powell said the double-time provision was not a mistake and "reflected the true intention of both APEX and the board".
The board's negotiator, Craig Coburn, said he could not remember the negotiations, particularly any dispute over the overtime pay, and had lost all documents related to the negotiations in the Christchurch earthquake.
Mr Dumbleton said there was no legal reason why the board should rectify the collective agreements to reflect the lower wage.
Dr Powell said the union had offered to settle with the board for between $120,000 and $150,000, based on workers' average number of times on the roster and the average number of callouts they would have had to attend.
"They declined that offer."
She said one of the reasons the error took so long to pick up was because staff payslips were very hard to decipher.
"They trusted their employer does the right thing." APNZ