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One of the country's biggest employers, with 21,500 workers, also has 24 staff on at least $1 million - one less than in 2017.
The average annual salary in 2017 was $50,000. The top earner at the co-op is, unsurprisingly, its chief executive.
Departing Fonterra boss Theo Spierings netted $8m in the year to June, slightly down from the $8.3m he banked during 2017.
There were 23 people below him earning over $1m and two who earned more than $3m.
The proportion of Fonterra staff who earned more than $100,000 grew in 2018.
Six thousand broke through that threshold in 2018, while the co-op's overall staff count only grew by 100 to 21,500.
According to financial statements, 5245 Fonterra staff earned more than $100,000 in 2017.
Air New Zealand, which employs 12,000 people, pays 4200 staff over $100,000.
Fonterra has reported a net loss of $196 million for the July year - its first annual loss since its inception in 2001.
The previous year's net profit was $745 million.
The co-op said its normalised earnings before interest and tax was $902 million, down 22%
Fonterra said its total cash payout for the year would be $6.79, comprising a Farmgate Milk Price $6.69 per kgMS and a 10c dividend.