Staff at a Monash IVF laboratory in Melbourne on Thursday transferred the wrong embryo to a woman, giving her one of her own rather than one from her partner, as they had requested.
The pair is believed to be in a same-sex relationship.
The company, based in Melbourne with clinics nationwide, apologised to the couple and launched an internal investigation.
But the Victorian Health Regulator has swooped in with its probe of Monash IVF and how the error occurred at its Clayton site.
State Health Minister Mary-Anne Thomas said the mistake was "completely unacceptable" and the company must provide answers.
"This will be quite devastating for the couple at the heart of this," she told reporters on Tuesday.
"We all know that the IVF journey can be a very long, torturous one. It can be very expensive as well."
In a notice to the stock market, Monash IVF announced that it would implement additional verification processes and patient confirmation safeguards.
It has informed the Reproductive Technology Accreditation Committee certifying body and insurers, declaring it expects the mix-up to fall within its insurance coverage.
The company's profit guidance remains unchanged, but the news sent its share price tumbling by more than 26 per cent to below 55 cents as of 3 pm AEST.
Monash IVF revealed in April that a woman at a Brisbane facility had another patient's embryo incorrectly transferred to her because of "human error".
With AAP.