The World Trade Organisation has upheld New Zealand's challenge to barriers that have cost the beef sector up to $1 billion.

Trade Minister Todd McClay hailed the WTO decision against the Indonesian non-tariff barriers as important for New Zealand farmers and exporters, and also trade fairness.

"We are committed to pursuing a range of options for addressing trade barriers that affect New Zealand exporters, including WTO dispute settlement as a last resort.

"As a result of this process, we have already seen some improvements to Indonesia's regulations and gains for New Zealand exporters to Indonesia. These will only improve following implementation of the WTO decision."

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New Zealand and the United States brought the WTO case against Indonesia in 2013, in response to 18 agricultural non-tariff barriers imposed since 2011, including import prohibitions, use and sale restrictions, restrictive licence terms and a domestic purchase requirement.

McClay said the barriers are estimated to have cost the New Zealand beef sector between $500 million and $1 billion. As recently as 2010, Indonesia was New Zealand's second-largest beef export market by volume, worth $180 million a year.

Indonesia can appeal the WTO decision. McClay said the NZ-Indonesian relationship remained strong.

"Even close friends have occasional disagreements and the WTO helps insulate trade policy differences from wider bilateral relations."