The miniature flags had initially been put out as table decorations on Thursday as part of an Olympic Games-inspired barbecue to mark the last day of parliamentary business before the summer recess.
They formed the centrepiece of decorations which also included red, white and blue balloons and cut-out Olympic torches on the walls.
However, the use of the union flags upset some SNP MSPs, who want to see Scotland become independent of the United Kingdom, and led to a confrontation with the canteen manager.
Former arts minister Linda Fabiani and Paisley MSP George Adam waved the flags and told him: ”These are not Scottish.”
The exchange was witnessed by Tory MSP Mary Scanlon, who confronted the pair and urged the catering boss: ”Just ignore these Nationalists.”
Within minutes of the altercation, staff returned to the canteen and removed the flags.
One said: ”We’ve had complaints. It’s all for this independence nonsense. It’s not all Rule Brittania and God Save the Queen it’s meant to be about the Olympics and Team GB but it’s just not worth the hassle.”
Other colours of balloons were also added to the display so it was not just red, white and blue.