Last year, the talks floundered to the relief of Irish farmers and the agri-food industry which claimed the proposals would have decimated their sectors.
Dr Walker replaces fellow New Zealander Crawford Falconer, who has returned to Wellington to become a deputy secretary at the Ministry of Foreign Affairs and Trade.
The WTO, a global body of 153 member states which deals with the rules of trade between nations, said Ambassador Walker will step into the lead role in talks that are the key to an agriculture deal.
An economist, he has a 20-year career in trade and economics, almost entirely in the Foreign Affairs and Trade Ministry in Wellington, and including a brief period with Telecom New Zealand.
Before his appointment as New Zealand ambassador to the WTO, he was principal economic adviser at the ministry.
He led free-trade-agreement negotiations with China and other trading partners. His postings have included London and Washington.
Meanwhile, it has been reported the United States and the European Union have agreed to continue talks to resolve a two-decade-old beef dispute and delay retaliatory US duties on EU products by at least two weeks.
Sources in Brussels said the deal under discussion could expand the EU’s quota for high-quality beef to 50,000 tonnes in three separate stages in exchange for the United States removing tariffs. The beef dispute goes back to the late-1980s, when the EU banned beef from cattle raised with artificial growth hormones, a common industry practice in the US and Canada.