The gaffe comes amid social media campaign #KeepScotlandTheBrand, in which users point out and protest instances where they believe Scottish branding is being replaced with British alternatives in packaging and marketing material.
One Twitter user asked Tesco whether it had done this.
Can you confirm that you are removing the Saltire from Scotlands produce and replacing it with a British flag @tesconews— Casper (@Casper10666) October 30, 2017
A now deleted response from the @Tesconews account said: "We are removing the Scottish Saltire and replacing it with the United Kingdom flag."
Tesco has since explained that this copy was designed as its response to a similar issue in August 2016, when its Scottish strawberries were relabelled as British, but was still accessible on an internal system to the customer services team running the account.
A spokesman said: "We are extremely proud to be Scottish agriculture's biggest customer, as any customer visiting our stores or buying our products in Scotland will see.
"There has been no recent change to how we use the saltire to celebrate Scottish food and drink."
The mini-debacle has been reported in Scottish papers The National and The Herald.
Twitter being Twitter, the brand has had to deal with a lot of anger and threats of withdrawing custom - with Tesco's response, and the difference between 2016 and 2017, seeming to fall on deaf ears.
Dear Tesco, shame on you! As you've banned the Saltire on Scots goods, I and 3 others will boycott your stores. We'll cancel home delivery, due Thursday, & shop where Scots producers & goods are clearly valued. #BoycottTesco #EveryLittleWorks— Paddy030750 (@paddy030750) November 1, 2017