MPI had temporarily suspended export certification to these markets, the ministry's response controller David Yard said.
Tomatoes can still be exported to countries which do not consider PepMV a quarantine concern.
"While PepMV can affect tomato production, it does not present any food safety concern or risk to people.
"New Zealand grown tomatoes are perfectly safe to eat," Yard said.
PepMV appears to have minor effects on the leaves of young tomato plants, but can cause mottling of the fruit on mature plants.
"It is uncertain how it would affect production volumes," Yard said.
MPI is trying to prevent the spread of the disease and ascertain the scale of the problem.
New Zealand Gourmet production director Roelf Schreuder said he was very concerned about the potential effect of the disease on the company's eight hectares of tomato plants.
Schreuder was doing everything he could to keep pepino mosaci out of his greenhouses. Only staff were allowed into the company's operations, he said.
"We dip all the crates and pallets that we receive in bleach to disinfect them.
"We've got strict hygiene instructions to our staff and as it can spread through tomato fruit, we give all our staff as many tomatoes as possible so they don't buy tomatoes in the supermarket and bring the disease to work on a sandwich."
A vaccine to control the virus was available, Schreuder said.
"You vaccinate young plants with a strain that's not as virulent, so that it doesn't show any symptoms and it takes the place of the virulent strain.
"That way you can protect your crops and we need to have that vaccine here as soon as possible."
Tomatoes New Zealand general manager Helen Barnes said they were still working out what strain of the virus had entered New Zealand.
Barnes said it was unlikely the disease could be eradicated, because it had already infected several sites.
"Our focus will really be on minimising the impact on our sector and that comes back to growers practising really good hygiene.
"Businesses can increase hygiene at all stages of crop production, restrict access to glasshouses to essential staff and ensure secure disposal of glasshouse waste to landfill," she said.
The affected facilities can continue production and sell tomatoes under strict biosecurity measures.
- RNZ
