Canterbury-based Synlait and Auckland's New Image are among the companies who did not make it on to the list.
Many New Zealand infant formula brand owners who do not operate factories are also yet to gain registration.
The new Chinese requirement could prove a major difficulty for unregistered companies that currently have product in transit to China - or at the Chinese border - that was previously understood to be able to enter the country under the new rules.
New Zealand Infant Formula Exporters Association chairman Michael Barnett said infant formula exporters would end up with product stuck at the Chinese border as a result of this new development.
Kiwi meat exports were held up at the Chinese border for weeks last year as a result of confusion over import documentation.
"We lost a whole lot of ground this morning," Barnett said.
Knox told the teleconference that he understood the latest regulatory change came about " as a result of differences of view between the technical departments in the China system".
"Unfortunately no one decided to tell us of this change before it was published on Sunday."
Knox said New Zealand officials had reached an agreement with their Chinese counterparts to "deal with product that is in transition on a case-by-case basis".
The Chinese authorities were willing to consider information about product produced by non-registered manufacturers that was held up at the border, in transit to China or about to leave New Zealand, he said.
New Zealand's retail-ready infant formula exports are worth around $200 million.
The Ministry said last week that the manufacturers that had already achieved registration were responsible for around 90 per cent of this country's baby milk exports.