At this week's hospital advisory committee, patient services executive director Lexie O'Shea said the board appeared to have failed to meet targets for some patients, resulting in some health measures turning "red" in August and September.
Results were not included in the committee papers as they take six weeks to compile.
If the situation was not reversed this month, the board could lose incentive funding for elective surgery.
The two measures coded red - meaning too many patients did not receive services on time - were first specialist assessments within six months, and patients who have been given a commitment not being treated within six months.
Mrs O'Shea told the Otago Daily Times the situation was exacerbated by winter, when acute hospital admissions were higher.
Board chairman Joe Butterfield told this week's meeting it "would be nice" to find some elective surgery cases had been wrongly coded as acute cases. The health funding model favoured elective work rather than acute treatment, he suggested.
Mrs O'Shea said staff were focused on better understanding the acute workload, so clinicians could make the best useof operating theatres.
A report to the committee said there was a particular issue with the board's ear, nose, and throat service, which was under pressure from skin lesion excision referrals.
"This is currently being discussed with funding and planning to explore options," the report said.
