Alliance has confirmed it will be closing its butcher shops at Oamaru and Timaru.
Alliance said two jobs at the Pukeuri butcher shop would go but affected staff may be able to work elsewhere at the Pukeuri site.
Alliance NZ general manager sales John Skurr said it had carefully considered feedback and the options, following its review in the past month.
However, the company had decided to close its face-to-face operations at Pukeuri and Smithfield.
Mr Skurr said the decision to close the local butcher shops was to help better concentrate on their primary business.
"While we remain committed to our online shop ... its operations will transition to an external provider," he said.
"I’d like to acknowledge and thank the butcher shop teams for their commitment, hard work and passion serving both local and online customers.
"Throughout this transition, our priority is to ensure that everyone involved is treated fairly and with respect," Mr Skurr said.
Meat sales to local customers will still be available online via the puresouthshop site.
This would ensure "an effective online service" for those wanting to buy Alliance products.
Shoppers at Pukeuri who spoke to Allied Press expressed disappointment.
Elly Toft , a regular shopper of Oamaru, said she was "really disappointed".
"I always stock up here because it’s so much more affordable than the supermarket."
She wondered if the same range and prices would be available online.
Regular shopper Rex Miller, of Twizel, was annoyed and had always rung ahead to see if the store was open.
NZ Meat Workers and Related Trades Union national secretary Daryl Carran said the affected workers were not covered by the Alliance collective agreement but the company still had an obligation to redeploy affected employees at both sites.
At this point any issue with that had not been flagged.
Closing these last two remaining butcher shops continued a trend by Alliance, he said.
Previously they had operated outlets at Invercargill, Lorneville and Mataura, Mr Carran said.