The 98-page report covers a wide range of topics including animal welfare, biosecurity, water, climate change and community development.
Fonterra's director of sustainability, Carolyn Mortland, said its environmental ambitions and targets required the most effort.
"This report shows we've got some work to do to reduce our environmental impact, and a great role to play in providing people with natural and nutritious food. "We really need to reduce our environmental impact... our focus is on climate change, water and waste,"
A further eight farmers were handed notices for not meeting farm effluent requirements.
Ms Mortland believed this showed the company was getting tough on farmers who weren't meeting their environmental obligations.
The report also noted that 99.6 percent of farmers now had fencing in place excluding their dairy cattle from permanent waterways on their farms.
"We think this actually reflects where we stand now and where most farmers are asking us [to be,] which is to be tough on those who haven't quite completed the requirements that most other farmers are at,"
- All stock must be excluded from any permanently flowing rivers, streams, drains and springs, more than a metre wide and 30cm deep
- All lakes must have all stock permanently excluded
- Any significant wetlands, as identified in your regional plan or policy statement must also have stock permanently excluded.