Fonterra CEO Theo Spierings offered the apology after traveling to China, where traces of a bacteria that can cause botulism were found in three batches of the company's whey protein concentrate, The Wall Street Journal reported.
The products were manufactured in May 2012 and the bacteria was identified this March. Extensive testing had been carried out since then, Spierings said. Customers were notified when the source of the problem, a dirty pipe, was identified July 31.
Spierings said milk powder and cheese products made by the company were safe.
News of the tainted products caused China to ban Fonterra's whey protein products and powder used in infant formula.
Chinese authorities have increased inspections of New Zealand dairy products, and signaled that extra testing may be necessary.
Dairy products represent about 25 percent of New Zealand exports.
Fonterra said New Zealand authorities had informed the company a blanket ban was not being imposed on the company's products.
"We have been told that MPI [Ministry for Primary Industries] is not aware of any additional market closures," the company said in a statement. "It is, however, getting clarity on reports that Russia appears to have put a temporary ban on New Zealand dairy products."