The Ministry for Primary Industries had previously paused some Australian exports but was still allowing tomatoes in from Queensland, where the virus is not present, and was testing seeds which can also contain the virus.
Tomato brown rugose fruit virus (ToBRFV) which affects tomatoes, capsicums, and chillies, has been found in two properties in South Australia.
The virus causes spotting, discolouration and deformities, impacting the fruit's market value - it has no impact on human health.
Tomatoes NZ chairperson Barry O'Neil told RNZ greenhouse tomato growers were really concerned about the discovery.
"If ToBRFV was to get to New Zealand, it could have dire consequences for our greenhouse tomato and capsicum industry because the virus spreads extremely easily and has such a major impact on production, with reported crop losses of up to 80 percent.
"The best line of defence is to keep the virus out of New Zealand. We are in discussions with government officials and the industry about how to achieve this."
O'Neil said the second-best defence was for growers to follow strict hygiene measures to try and stop ToBRFV from entering a particular property, if it did arrive in the country.
