Limited new access was gained into the highly protected dairy markets of the United States, Canada, Japan and Mexico.
''Entrenched protectionism'', demonstrated by the US dairy market in particular, ensured the dairy deal failed to reach its potential, Fonterra chairman John Wilson said.
He acknowledged the efforts of Trade Minister Tim Groser and his negotiators to get some gains in market access for farmers, saying it had been an ''enormous undertaking''.
''Dairy has been very hard to resolve and New Zealand has managed to get some progress against the odds,'' Mr Wilson said.
While very disappointed the deal fell ''far short'' of TPP's original ambition to eliminate all tariffs, there would be some useful gains for New Zealand exporters in key TPP markets such as the US, Canada and Japan.
Greater benefits would be seen in future years as tariffs on some product lines were eliminated, he said.
Dairy Companies Association of New Zealand (DCANZ) chairman Malcolm Bailey said it was always going to be very hard, given the starting point for dairy as one of the most protected sectors globally.
While further market opening was needed to help address price volatility in the global dairy market, the deal did contain some useful improvements, Mr Bailey said.
DCANZ, which represents the collective public policy interests of its member dairy companies, would undertake a complete assessment of outcomes as fuller details of the deal for dairy became available.
Removal of distortions from global dairy markets remained a key priority for DCANZ.
It would be looking closely at the trade policy landscape over the coming weeks, and talking to the Government to ''define a pathway forward'', he said.
DCANZ would undertake a complete assessment of outcomes as fuller details of the deal for dairy became available.
The good outcomes for other agricultural exports would help demonstrate that free trade should not be feared and, by doing so, create a platform for further opening of dairy markets, Mr Bailey said.
Melbourne-based Rabobank dairy analyst Michael Harvey said the agreement's outcome was ''pretty disappointing'' from a dairy perspective.
But New Zealand did have preferential access into China, the world's largest importer of dairy products.
It had access to a lot of key markets that mattered and it was well placed to serve key growth markets, he said.
Federated Farmers president William Rolleston said the deal, although not as comprehensive as the organisation would have liked at the outset, appeared beneficial for agriculture and New Zealand.
While it would have been great to see dairy tariffs eliminated altogether and for a greater range of products, preferential access to new dairy quotas into those markets should be helpful.
''Overall, dairy will still reap the benefits of tariff savings into other TPP markets and further progress on dairy access can be made in the future,'' Dr Rolleston said.
Opponents of the TPP should consider the ''serious consequences'' that would be faced by New Zealand if it was not part of such a trade agreement, should the Government be unable to secure Parliamentary agreement.
''In other words, while we still await much of the detail, it's clear that we are better off today than we were yesterday. The conclusion of the TPP negotiations is the start of a journey of trade liberalisation, a journey some countries find harder than New Zealand,'' Dr Rolleston said.
