The affected product is Nutricia Karicare follow-on formula for children from 6 months old, the ministry said.
"Nutricia has advised that three of those [five] batches are in a warehouse in Auckland, one is on a ship, and the other is in storage in Australia," said the ministry's acting director general, Scott Gallacher.
"Nutricia has advised it has locked down those batches, and they will not be sold on the market ... MPI is still in the process of verifying this information, and today sent a team to Nutricia's Auckland warehouses."
Gallacher said that until the verification process was completed, parents should use Karicare formula for children 0-6 months or an alternative brand.
Fonterra says eight of its customers are potentially affected by the contamination of three batches of WPC80 whey protein, manufactured in May 2012, which are suspected of containing a bacteria that can cause botulism, a potentially fatal illness.
The whey protein is used to make a range of products, including infant formula and sports drinks.
A dirty pipe at Fonterra's Hautapu plant has been blamed for the contamination.
- Christopher Adams
