The flag has been replaced with the union jack on boxes of strawberries and raspberries grown north of the border.
Tesco's official Twitter account told one customer that the move followed complaints from English customers.
But a spokesman for Tesco denied that, and insisted that it was intended to "provide consistency".
The decision emerged when one customer tweeted Tesco to ask why the Scottish flag no longer appeared on her raspberries.
When the supermarket's official Twitter account replied, they told her they had received "several customer complaints".
They said some customers were annoyed that an English flag was not shown on berries grown south of the border.
And when the packaging was re-designed, they decided to remove the saltire to avoid further complaints.
However the customer was told that each punnet of fruit clearly showed where the berries were grown.
The series of tweets have provoked a storm of criticism on social media, with many people urging Tesco to reverse their decision.
A Tesco source said the tweets had been sent in error.
And a spokesman for the firm said: "To provide consistency for customers, we mark all of our homegrown fresh berries with a union flag.
"The country of origin is also clearly displayed on pack."
Supermarket giant Tesco has been criticised after it admitted removing an image of the Scottish saltire from punnets of Scottish berries.