Its investigators face 2037 open files, almost two-thirds - 63 per cent - more than this time a year ago.
"We recognise the impacts that delays have on consumers and providers," HDC said.
An HDC email to one complainant advised them it was now consulting with the agency's in-house clinical adviser about all the information so far gathered.
"Given the high volume of complaints we have at this stage, this part of the process may take a number of months," it said.
"We thank you for your continued patience and will keep you updated."
HDC told RNZ it was still closing investigations at a rate similar to previous years: 71 per cent within three months, 78 per cent within six months, and 87 per cent within 12 months.
This added up to a record 2627 complaints closed in the 2021-2022 financial year, up nine per cent.
The increased load was "primarily due to Covid-19's impact on the health and disability system".
It was working to streamline its processes and ensure early resolutions where possible.
An early resolution was not a soft option, it said.
"Where appropriate, [it] can result in the best outcome for all parties," the commissioner said in a statement.
"It can ensure the consumer's resolution outcomes are met in a timely and direct manner, and can also assist to restore or strengthen the relationship between consumers and providers."
Four out of 10 complaints involved direct resolution between the provider and complainant, who could tap the Nationwide Health and Disability Advocacy Service.
Both that service and the provider had to report back to the commissioner, "ensuring that people's concerns have been addressed appropriately".
HDC cited two case studies of early resolution, one about lack of mental health support and the other about a delay in getting blood cancer treatment.
"The provider gave a detailed explanation of what had caused the delay, and an outline of the steps taken to mitigate further instances of delay, and also provided the consumer with a letter that she could give to her employer to explain why she would require additional time off work," its summary on the latter complaint said.
- RNZ