Waddell confirmed no Kiwi athletes were being considered close contacts.
New Zealand's presence in the Olympic Athletes Village in Tokyo has swelled by more than 150 following the arrival of swimmers, boxers, rowers and hockey players yesterday.
It coincided with a second case of Covid-19 being identified elsewhere in the village.
Games organisers won't say who has contracted the virus, other than that both cases are from the same team and sport.
Details are also light about 25 other Games-related cases recorded around the city, four days out from the Opening Ceremony.
Organisers today reported 10 new cases connected to the Olympics, including a third athlete who was not staying in the village.
New Zealand chef de mission Rob Waddell told RNZ the situation was concerning, but not unexpected.
"I guess any Covid outbreak is always concerning, there's a wide range of reactions within the village.
"I think countries that have been living with this for a long time, so it's no big deal. We've anticipated and been realistic that Covid will be at some point in the village and so for us we're just trying to stick really well to our protocols and obligations that we keep everyone safe."
Using face masks, hand washing and social distancing were the three main ways the team aimed to avoid infection, along with staying away from shared spaces as much as possible, he said.
No members of the New Zealand team were close contacts of those infected in the village and team were not aware of who those infected people were.
The International Olympic Committee (IOC) had been transparent, had contact-tracing systems in place and, although the situation wasn't ideal, Waddell said he believed the prevention measures put in place would work for the squad.
"It seems all countries are adhering to that and being very respectful," he said.
"We're confident the team's turning up in good shape, they're safe to create the performance environment that we know is really important to the team and those who are arriving are knuckling down and getting on with the job. There's a real sense of excitement to be here, but we know with all the distractions going on in the world it's important to focus on what matters."
The Football Ferns have arrived and will play their first pool game on Wednesday against Australia.
"We welcomed them in yesterday and they're really keen to get on with it and I know they've been working hard and they're looking trim and fit and ready to go," Waddle said.