The World Trade Organisation has upheld New Zealand's challenge to 18 agricultural non-tariff barriers imposed by Indonesia.

New Zealand and the United States jointly brought the case against Indonesia in 2013 over a range of barriers imposed on agricultural imports since 2011.

They included import prohibitions, use and sale restrictions, restrictive licence terms and a domestic purchase requirement.

Trade Minister Todd McClay says they've cost the New Zealand beef sector alone between half a billion and a billion dollars.

"This is an important result for New Zealand's agricultural exporters, and for trade fairness," he said on Friday.

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

Mr McClay has given an assurance that New Zealand still has a very strong relationship with Indonesia.

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