Peek said they had to be mindful that there might be people who, for example, gave sperm samples while undergoing cancer treatment as young men who might be overseas.
"Unless we do something on their behalf it will be too late," he said.
Some of the samples dated back to 1988 so there had been "a bit of detective work" involved tracking down the owners.
Peek said more than 500 people had agreed to have their material discarded. A further 200 had applied to the Ethics Committee themselves.
Fertility Associates hadn't had responses from about 900 people.
However, about 600 of those had signed for their notification letter indicating they were aware of the deadline.
It was thought the other 300 were not aware their samples were due to be disposed of. Many of those would have more than one sample in storage, he said.
For some people, the decision on what to do with their material was "very difficult".
"It can be a very emotional process," he said. "Sometimes I think they'd rather just not get in touch and let us get on with it."
Peek said the deadline might have prompted "one or two" people to undergo invitro fertilisation (IVF) treatment, but he could not be sure whether that was just a coincidence.
In 2004, the Human Assisted Reproductive Technology Act was passed governing the practice of fertility treatment. In 2010 the legislation was amended allowing the retrospective 10-year storage period for eggs, sperm and embryos.
At least two other clinics, Fertility Plus at Auckland's Greenlane Hospital and Otago Fertility Services in Dunedin, also hold embryos which may be affected by the deadline.
