After a total of 24 rats were captured — the Dunedin supermarket successfully passed a 48-hour "clear air period" on Wednesday that allowed it to resume trading after being closed for 18 days.
New Zealand Food Safety (NZFS) deputy director-general Vincent Arbuckle said the agency anticipated its investigation could take "up to several months" due to the complexity and need for thoroughness.
"Such investigations must be done thoroughly and fairly so that problems can be prevented from recurring," he said.
There needed to be "increased vigilance" by Woolworths of its South Dunedin store to ensure the pest control measures in place continued to be effective.
Mr Arbuckle said the reopening of the store had not affected the investigation, as the causes and scale of the problem at the supermarket remained the same.
NZFS would receive daily updates from the store for a period and food safety officers would conduct regular follow-up visits so consumers could have confidence that Woolworths was ensuring food at the store was safe.
He said these visits would either increase or decrease according to its confidence of Woolworths’ food safety management.
Mr Arbuckle said the news about Countdown’s rat issues had signalled the importance of food safety to other businesses.
"All food retail businesses have a legal obligation in respect of food safety and the expectations of consumers," Mr Arbuckle said.
"The pest-management issues that Woolworths has responded to at its Dunedin South and other stores over recent weeks have highlighted the importance, for all food businesses, of having an active and scalable pest-management programme.
A Woolworths New Zealand spokeswoman said it was very pleasing to reopen the store.
"It’s been fantastic to see so many of our local community popping by to say hello and we’re looking forward to further building back trust and confidence with customers in the coming weeks and months."
The store would continue to work closely with Rentokil and NZFS to ensure the pest management processes kept working.
The spokeswoman said Woolworths would no longer be commenting on the affairs of Countdown Dunedin South now that it had returned to usual trading.