SNP MSP Christine Grahame said the National Library of Scotland should allow the member of staff to display the Saltire at work
The National Library of Scotland told a staff member to remove Saltires from his desk as they may intimidate non-Scottish workers, an MSP has learned.
SNP MSP Christine Grahame said the instruction to remove the flags was issued by the library's director of customer services.
Ms Grahame described the policy as an "unacceptable slur" on Scotland's national flag.
The library said the worker's display of flags had been "excessive".
Ms Grahame used freedom of information laws to obtain copies of a string of e-mails sent by director of customer services Alexandra Miller to National Library of Scotland (NLS) staff and managers over the issue.
In the e-mails, which have been seen by BBC Scotland, Ms Miller told colleagues that displaying the Saltire or other Scottish symbols "could even impinge on respect at work issues where such nationalistic displays may intimidate non-Scottish colleagues".
She added: "I am very disappointed to see that (the member of staff) continues to have inappropriate material bedecking his workstation. This includes several Saltires and a Lion Rampant, and the personalisation of a chair with red tartan."
The e-mails show that Ms Miller personally removed "three or four" Saltire flags which had been put up by the member of staff, and she pointed out in one message: "NLS flies the UK and Scottish flags on our buildings and that is where they belong."
In another e-mail, she said: "Workstations are the property of the library, not of individual members of staff, and it needs to be clearly understood that things of this nature are simply not allowed, for the reasons already given. This applies to any inappropriate material including calendars and any items that could be deemed to be racist, sexist etc."
The e-mail exchanges also reveal that another member of NLS staff said the worker concerned "does not understand why his desk has been singled out when many of the library's desks have been personally adorned".
Ms Grahame, who became aware of the issue after being contacted by a member of the public, said the policy was "deplorable and completely out of touch".
Calling on the library to apologise, she added: "This is a completely unacceptable slur on Scotland's national flag.
"I would have thought that in the National Library of Scotland of all places they would have understood and appreciated the place the Saltire has in Scottish hearts as one of the oldest national symbols in existence.
"Instead it appears that senior management have embarked on a deliberate assault on the flag of Scotland, trying to purge it completely."
Calling for an apology from the library, she described the actions as "utterly disproportionate".
However, Martyn Wade, the national librarian and chief executive of NLS, said it did not, and would not, "ban" staff from displaying the Saltire in the workplace.
He added: "We merely asked a single individual to remove what we considered to be an excessive display of large flags from a desk in a shared, professional work area, and we would have done so regardless of what the flag was or indeed any other adornment.
"The National Library of Scotland is immensely proud of our place at the heart of Scotland's culture and knowledge, and indeed we proudly fly the Saltire from our main building."