While the scare turned out to be a false alarm, the Ministry of Primary Industries laid four charges against the company, including exporting a product that did not meet relevant standards and failing to tell authorities about a potential problem as soon as possible.
Fonterra said it would not contest the charges, which each carry a maximum penalty of New Zealand dollar 500,000 (USD 427,000).
"We have entered guilty pleas," Fonterra spokeswoman Maury Leyland told public radio.
The sector is crucial to New Zealand's economy, with dairy exports in January alone totalling about NZ$1.7 billion, almost half of which went to China.
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The scare erupted in August last year when Fonterra announced a whey protein used in baby formula and some other products had tested positive for a bacteria linked to botulism, which can cause paralysis or death.
It led to infant formula being pulled off shelves from China to Saudi Arabia before subsequent tests determined the bug was actually another, non-toxic, bacteria strain.
"Food quality and safety remain our top priority, and are fundamental to our business," Leyland said.
"New Zealand's dairy food production and safety systems have been affirmed by both the (Fonterra) board and government inquiries as being as safe as any in the world.