Greenpeace campaigner Amanda Larsson said setting the targets was an important first step, but Fonterra seemed to be "in denial of the fact that taking action on climate change means reducing the dairy herd".
Greenpeace said in a statement that new figures from climate scientists showed human-induced climate change was happening faster than ever.
Larsson said Fonterra's proposed approach to reducing the bulk of its emissions was too risky.
"We urgently need a dramatic reduction in greenhouse gas emissions from livestock. The only way to do that in the time we have available is to reduce the herd."