Sami said the flag made her feel "very uncomfortable" and asked the store to "please take it down".
"It is a sign of hate and white supremacy worldwide and I believe it has no place in our country," she wrote in an email to the store manager.
"Please put yourself in the shoes of those targeted by the extreme ideologies this flag represents before you reply."
After the first comment from the store clerk, and following Sami's email, the store agreed to immediately take the flag down.
"I felt like their response was slack and lacked understanding. I was upset because my friends had messaged me their responses and they had told them the flag had been taken down and stock removed and that they were sorry," Sami said.
In their response to Sami, the store also said the flag is admired by a number of "Americana enthusiasts and Dukes of Hazzard fans who buy it, that are not racists".
She adds that this isn't the first time she complained about the flag.
"If they truly stood by their words, the confederate flag would have been removed years ago. I have complained before."
"They made a statement on Friday but still had the confederate flag available for purchase right up till we asked them to remove it. Is this a company that is aware? Is this a company re-evaluating their part in supporting racism and hate? They don't acknowledge that. Don't get me started on the Dukes of Hazzard argument. It IS a racist symbol even if you watched it on TV growing up with no idea - you know it's meaning now. Wake up," she added.
"We let this racist stuff slide and it's up to us to ask these people why they think this? What are their reasons? It's important to share why it hurts you and to have examples to support yourself, and try and keep it a conversation," she said.
"It's a lot of work and it makes me want to cry with frustration but I hope it can help to open up people's perspectives and gain understanding of each other.
Kotahitanga, We are one. Warts and all."
Contacted by the Herald, the store confirmed the flag had been taken down immediately after the email exchange.
"We should have taken it down a long time ago," Army and Outdoors' owner Jason Robinson said.
"Neither the owner nor the employees of Army and Outdoors endorse or promote hatred of any kind. Furthermore, we are deeply saddened by what has happened in Christchurch. We offer our deepest condolences to the victims and families of the Christchurch shooting today. We hope everyone is safe and that justice prevails. There is no place for this violence in NZ or anywhere for that matter," he added.
The confederate flag was for sale in the store, along with a number of other country flags, for $19.90.
The store says it has now put a New Zealand flag where the confederate flag used to be.
