The document, which was leaked to RNZ, stated cleanliness and pest control review would be carried out next week.
It comes after rodents were found at two Woolworths stores in recent weeks - as well as one Pak'n Save store.
At least 24 rats have been caught at Dunedin South Countdown over the past week.
Meanwhile, a mouse was seen scurrying through the deli cabinet at Eastgate Countdown.
The Dunedin store remains closed until there is a 48-hour period with no rodents captured.
Individual store teams and managers were required to read and sign the memo as being understood and actioned by Tuesday.
The memo required the duty manager to enter details in a "pest sighting register" as soon as as a report was made.
"They will also review the surrounding areas for immediate cleaning opportunities," it said.
The duty manager was then required to escalate the issue to store manager.
The memo said food debris, cardboard and general rubbish created places for pests to nest and increased the risk of pest activity.
Staff were asked to check "high risk areas" daily.
These included bulk food storage and bins, grocery, sugar, flour, prop bread, pasta, pet food and cereal sections.
"Look under bins on shop floor for dropped food."
Staff were also asked to look for bakery flour and ingredient residue on floors.
"All bins should be enclosed and have lids and external doors to should be kept closed as much as possible."
The memo asked cleaning and rosters to be followed "as required in the food safety manuals".
