The other case is a Belgian traveller who left New Zealand on August 6 and transited through Singapore en route to Amsterdam. Both travellers were asymptomatic in New Zealand.
An interview with the cases, now overseas, established that the Japanese traveller spent some time in Wellington prior to departure and visited The Ramen Shop among a number of other places.
"These premises are all considered casual contacts of the traveller, they have been contacted and provided with advice as part of the normal contact tracing process," the ministry said.
"No further action is required from any of these premises as the risk is considered very low."
The Ramen Shop in Newtown posted the notice on its Facebook page about the same time as today's 1pm press conference started to update daily cases of the virus.
It said a person who had been diagnosed with Covid-19 dined there on August 5 between about 5.30pm and 7pm.
It said the individual was asymptomatic at the time.
"We have chosen to post this out of respect for our team and customers, we believe being open and responsible, following guidelines and expert advice is the way forward.
"We would like to send our best wishes to this individual, we hope you are doing ok, get well soon.
"Thank you for your efforts in contact tracing, you're doing your part to help many people and this deserves our thanks."
Asked about the Facebook post at today's 1pm press conference, Health Minister Chris Hipkins cast doubt on the case saying they were not going to comment on every speculation on social media.
"I've spent quite a bit of time running down allegations yesterday around positive cases in Wellington and none of them were true. So we have got a very consolidates process in place so when we do make announcements here that information is all correct and accurate.
The Ramen Shop has since posted again on its Facebook page saying they were surprised to hear about that "denial".
"Since then we have received many massages of love and support, which we value highly.
"Unfortunately some feel the need to make unhelpful and hurtful comments, this is not what our staff deserve."
The shop said it would continue to be open and honest about all the information is received and had no desire to spread misinformation.
Mayor Andy Foster said Wellingtonians should not be anxious about the case but continue to be aware of the gravity of the national situation.
"What it does confirm for us all is that we all need to practise the hygiene protocols that we were practising earlier this year.
"We are all now aware of the importance of contact tracing, I think people are taking that very seriously now, and that's what we need to do so that if and when there is a situation in Wellington it's easy to track people down who might have been in contact with anyone diagnosed with Covid."
Foster noted The Ramen Shop case was low risk and the person left Wellington some 10 days ago.
"This person has been through several situations in their travel where they are much more likely to have picked up Covid than having contracted it in NZ."
The shop said it was continuing to operate under Covid alert level 2 guidelines.
Meanwhile, there are 30 active cases connected to the recent outbreak which originated in South Auckland.
It has now extended to the North Shore and Tokoroa, which have confirmed cases.
Members connected to the outbreak have also visited Rotorua, Taupō and Morrinsville.