The woman and her husband's story started in June 2017 when a blood test conducted by Fertility Associates suggested she might already be pregnant.
Those results were not passed on to the doctor, who then approved the woman starting medication for her IVF cycle.
She had been on the treatment for just over a week when she discovered she was pregnant.
While HDC said the woman did give birth to a live baby, it is not clear from the report if the error impacted her pregnancy.
An HDC spokeswoman told the Herald: "The family did not report to the HDC that the baby suffered any harm."
The couple contacted Fertility Associates four times to express concern and was ignored each time.
"We have now asked four times to have the last cycle blood results, and it looks like
you have finally provided them but in your own spreadsheet as opposed to the
[medical laboratory's] format of the other cycles. It seems that you have been
withholding these results from us. Please send through the last fertility cycle blood
test results in the format as sent from [the medical laboratory]," the woman's husband emailed on the fourth attempt to contact Fertility Associates.
While the couple told the commissioner, they were "confident" that there had been a deliberate cover-up of the mistake, Fertility Associates said that was not true.
"We reject the accusation that we were somehow covering up providing the results to [Mr and Mrs A]," Fertility Associates told HDC.
A independent specialist assigned to review the case told HDC: "The bottom line is that [IVF] treatment should not have been started if staff were aware of the elevated progesterone levels."
The specialist said it suggested a lack of rigour in clinical practice by those making the decision to treat.
"The only excuse is that pregnancy in a couple with repeated fertility treatments is a rare event," the independent doctor said.
The Deputy Commissioner was also critical of Fertility Associates' failure to disclose the error.
"This case highlights the importance of robust test-ordering protocols and effective
communication between providers to ensure quality of services, as well as the importance of openly and honestly disclosing information about errors that occur during the provision of a healthcare service," Wall said.
As a result of the investigation, Wall told Fertility Associates to provide evidence of a new test-ordering protocol, and to conduct an audit of staff compliance with that new protocol in place.
She also recommended that it review HDC's Guidance on Open Disclosure Policies and
identify areas for improvement in its practice.
Fertility Associates was told by the deputy commissioner to apologise to the family.
In the report, a Fertility Associates spokesperson said: "It was not our intent to provide treatment that did not meet expectations, or to provide any additional stress during subsequent communications."