But NZF chief executive Andrew Pragnell feels their proactive handling of the situation will put them in a good place.
"There might have been some sides that would have played regardless and pushed on, thereby putting players at risk," said Pragnell. "We have already got really positive relations with those clubs and we will get a lot of respect for doing what was right. As soon as we knew, we stopped.
"Everyone in northern hemisphere football is used to dealing with Covid on a regular basis, as we have seen with the disruptions to leagues. But what I don't think would be well received is an attempt to shield or hide a scenario, or even worse put a top-flight player into a risky position when you had information.
"We can hand on heart go back and say we did the right thing and that will stand us in good stead."
The positive results came to light on Tuesday morning at the team base in Dubai. The source of infection is not yet known, with the team operating under the same health and safety protocols that NZF adopted at the Tokyo Olympics last year.
"Covid is rife throughout the world and we have seen multiple sporting teams get Covid but regardless, we will take a closer look at potentially where it could have come from and make sure the net is as tight as could be when it comes to future tours," said Pragnell.
Defender Nikko Boxall had been unwell earlier in the week, but it's understood he has tested negative for Covid.
It's a similar scenario for goalkeeper Stefan Marinovic, who joined the team on Sunday after recovering from Covid picked up on club duty in Israel, as it is believed he has also tested negative.
NZF are currently working on logistics and rescheduling flights. Members of NZF staff will remain in Dubai over the next week, until all players have been able return to their home bases.
Almost two thirds of the New Zealand squad are currently in their off seasons, which should minimise disruption to their club schedules.
"All going well, the potential impact on missing potential games is likely to be very small," said Pragnell.
Despite the unfortunate situation, Pragnell said there was a silver lining.
"It was a real shame to [cancel the game] but it was the only call that could be made," said Pragnell. "And it's an example where testing results and protocols have hopefully shown something up early that we have been able to act on really quickly and early and avoid spreading it to another team.
"This window has had its fair share of challenges but everyone did everything right in terms of getting the right outcomes that we could."