While New Zealand presently didn't have community transmission, Wilson noted that we need to be prepared for possible outbreaks from occasional border control failures.
"Having good public toilet facilities is important all of the time, because evidence make it very clear that norovirus outbreaks happen when people don't wash their hands after going to the loo," he said.
"And now we're in a pandemic, the Ministry of Health has put all of this emphasis on hand-washing, and as far as we could see, only one local authority - Napier City Council - actually boosted the level of soap in their toilets."
The survey also found just one in 10 toilets had the Covid-19 QR code posters and there were no toilet bowl lids in one third.
World Health Organisation guidance on hygiene around Covid-19 highlighted the importance of water and soap in facilities, along toilets being able to be flushed "with the lid down to prevent droplet splatter and aerosol clouds".
Further, fewer than 30 per cent of the toilets had "no touch" flushing mechanisms.
Wilson said while there had been modest improvements in the amount of soap provided, compared with a previous survey eight years before, there wasn't any more water.
"It's interesting that New Zealand is spending money on complex technologies like improving cancer screening - but here we are with toilets without soap," he said.
"If we're not organised to do the basic things, it's not a good sign."