FDA General Secretary Dave Penman has spoken to the Guardian in response to Ministers' disagreements over civil servants' involvement in the run-up to the EU referendum.
Penman said: "Government departments are not the playthings of individual Ministers and their own particular conscience with regard to the EU referendum."
He reiterated that "civil servants are there to support the Government of the day and that Government's policies, which in this case is to remain part of the reformed EU.
"Politicians' continued wrangling over this issue will only serve to impact upon the smooth running of government and damage the essential relationship between civil servants and Ministers.
"The FDA welcomes the clear guidance issued by Sir Jeremy Heywood, which clarifies the responsibilities of Ministers and civil servants," Penman added.
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EU referendum row could affect functioning of Whitehall, says union