New Zealand has signed a free trade agreement (FTA) with South Korea that cut duties by $65 million in its first year.

Trade Minister Tim Groser, in Seoul to sign the deal, said New Zealand paid $229m a year in duties on the goods it sold to South Korea.

The biggest beneficiaries of the agreement will be the beef and dairy industries.

South Korea is New Zealand's fourth-largest beef export market by volume, buying nearly $110m of exports in 2013.

New Zealand beef faces a 40 per cent tariff when it enters the Korean market, but the FTA will remove that over 15 years.

In 2013 South Korean tariffs on New Zealand's beef exports totalled about $43.5m, Beef+Lamb NZ said - effectively about $1.34 of additional cost per kilogram of carcase weight on beef products.

Dairy trade is worth $263m, with exporters at present paying tariffs of between 8 and 176 per cent.

New Zealand is playing catch-up with the deal, since competitors such as the Australia, United States, Canada, Chile, and the European Union already have FTAs with South Korea.

The deer and seafood sectors have complained they have been short-changed by the deal.

Deer Industry New Zealand said frozen deer velvet, which accounts for 75 per cent of $20m of velvet exports, had been completely excluded from the agreement. Processed (dried) deer velvet has been included in the FTA, but the phase-out period for the existing 20 per cent tariff is 15 years.

Seafood New Zealand criticised the deal for excluding frozen squid, which accounts for 28 per cent of seafood trade with South Korea and will continue to suffer a 22 per cent tariff.

Seafood exports are worth about $50m a year.