A spokesperson for The Executive Office said: “The document in question was commissioned by the Head of the Civil Service in May 2015.
“Officials prepare a range of papers on a regular basis, many of which are working papers and do not form submissions sent to Ministers.
“This analysis paper was not sent to Ministers for consideration following its completion.
“Following a Freedom of Information request to the Department, Ministers became aware of this work and the document was released on two occasions following Freedom of Information requests.
“The Executive Office could not have taken sides in the referendum campaigns in the absence of an agreed position. In any case the document contains well rehearsed arguments which were openly being aired during the referendum campaign and would have added nothing to the wider debate.”
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