Richmond Road Pharmacy is struggling with an influx of customers since the announcement.
Pharmacist Samantha Tibshraeny said there had been "no guidance" from the Ministry of Health on what being at level 3 meant for the business.
"It's absolutely nuts," she told the Herald.
"People are, like, swarming the pharmacy."
They have taken their own initiatives to allow only one customer into the store at a time, with one staff member in gloves and a mask serving people.
But Tibshraeny said they had been supplied with no protective equipment and were left in the dark over how to handle all the people coming in.
Pharmacy manager at Unichem Albany Metro Tania Iskenderian said she was the only in her pharmacy at the moment due to isolation rules, and was letting in one person at a time.
"They've been wanting their medication all at once," she said.
If a person needed their medication at that time they would receive it, but others would be told to wait until it was actually needed.
"There's no urgency, we're not going to close down," she said.
"We have plenty of stock, there's no shortage at all ... I am loaded with paracetamol and you name it, all the drugs that people are on regularly."
She was prioritising getting prescriptions to elderly customers.
Life Pharmacy Glenfield owner Seema Rambisheswar said they had been "snowed under" since Saturday's announcement on the alert system.
They were allowing only five customers in at a time, but people expected their prescriptions to be ready at once.
"It's just crazy here," she said.
Since today's announcement there had been more customers wanting retail items.
Rambisheswar wanted people to know the pharmacy would remain open, and there was no need to panic.
"We will be here for them," she said.
Dannevirke Pharmacy is also taking steps to protect staff and the community from Covid-19.
Clients wanting to visit the pharmacy are greeted at the door and asked if they are well, have travelled or been in contact with a person who has travelled in the last 14 days.
Pharmacy owners Hamish and Jess Pankhurst say Covid-19 is an ever-evolving situation so the pharmacy is ever evolving to ensure it can remain open.
"We have put measures on place to ensure our staff are kept safe and the community are kept safe," Hamish said.
"There will be disruptions but my focus is to keep everyone else well."
"We are looking at increasing our home deliveries and we have waived the fax fee on prescriptions."
He said the key message was that people shouldn't panic.
Numbers for Chemist Warehouses around the country reached a voicemail that the shops were experiencing "unprecedented demand for pharmacy items", including prescription medications.