He was a trainee specialist in pathology on January 25, 2012, when the women's breast-tissue specimens were processed as "urgent" at Southern Community Laboratories (SCL).
Mr Hill said human error caused the mix-up of the samples from patients X and Y, and although Dr H was responsible for the preparation of their specimens for processing, he did not know when or how the error was made.
The commissioner said that although it appeared an individual error had occurred, "the error was a result of a number of unsafe policies and practices in place at the laboratory at the time. Accordingly, I consider that the ultimate responsibility for the error must fall on the laboratory itself."
SCL chief executive Peter Gootjes said the company had apologised to the two women a number of times and again recently by letter at the request of Mr Hill.
He said no action had been taken against staff. "The focus was on system reviews and improvements as opposed to punishment."
Mr Hill said Mrs Y was 57 in 1999 when first diagnosed with cancer in her right breast. She had surgery and radiotherapy in 2000.
In January 2012, she had a biopsy that SCL wrongly said showed cancer in her left breast. She underwent a mastectomy. But analysis by an SCL pathologist of tissue taken during the operation found no evidence of cancer. This prompted cross-checks, which eventually showed Mrs Y's biopsy had been switched with Mrs X's and led to four formal inquiries.
Mrs X, aged 54 at the time, was diagnosed by SCL from her January 2012 sample as having a benign lump in her right breast. However, Dunedin Hospital doctors thought this inconsistent with other clinical information and asked for a second biopsy.
Two samples were taken in February 2012 and this time cancer was diagnosed in Mrs X. The following month she had both breasts removed at a private hospital.
Mr Hill said SCL had undertaken to make a number of changes, including ceasing to treat breast biopsies as routinely urgent because doing so had removed safety checks and was potentially dangerous.
Read more:
• Breast cancer mix-up still a mystery
The Southern District Health Board knew of the biopsy switch in March 2012, but did not tell Mrs X until June of that year, after Mrs Y indicated she wanted to speak with Mrs X and after the Herald on Sunday had publicised the error.
Mrs X told the commissioner she felt isolated, frustrated and hurt by the DHB's poor communication. Mr Hill said the DHB had apologised.
DHB spokesman Dr Richard Bunton told the Herald: "We were so concerned about the woman wrongly treated that we dropped the ball [regarding Mrs X]."
The sequence in 2012
January 25: Breast tissue samples from Otago patients X and Y are accidentally switched at Southern Community Laboratories (SCL). Mrs Y wrongly told she has cancer and Mrs X wrongly told a lump is benign.
February 16: Mrs Y has an MRI scan that shows no conclusive evidence of disease. She asks if a mix-up might have occurred. Southern DHB checks rule this out, but the lab is not asked.
February 23: MRI shows extensive cancer in Mrs X's right breast and possible abnormalities in left.
March 2: Mrs Y, who in 2000 had right breast cancer surgery, has an unnecessary left mastectomy.
March 8: Mrs X has bilateral mastectomy in a private hospital.
March 9: SCL pathologist reviews tissue from Mrs Y's surgery and reports absence of cancer cells.
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