Brexit secretary Mike Russell claimed it was the “wrong decision which needs to be changed”.
His comments were made after Holyrood Presiding Officer Ken Macintosh wrote to all MSPs on Thursday to inform them of the decision taken by the Scottish Parliamentary Corporate Body (SPCB).
The body, which makes decisions on the running of Holyrood and is made up of a representative from each political party, agreed the flag should be removed at 11pm on Friday, January 31.
Mr Russell said on Twitter: “The flag is not only a symbol of our solidarity with the #27 and all EU citizens in Scotland, it also represents our wish as a nation to return to membership of a union we never voted to leave.”
A Scottish Parliament spokesman said: “The decision taken reflects the legal position that the UK will no longer be a member of the EU from January 31.”
The European flag, with its gold stars on a blue background, was designed to stand for the “ideals of unity, solidarity and harmony among the peoples of Europe”.
It was was first developed by the Council of Europe in the 1950s and also adopted the EU some 30 years later.
In his letter to MSPs, Mr Macintosh said the SPCB had agreed that after Brexit, the Scottish Parliament “will no longer fly the EU flag on a daily basis”.
He added Holyrood will still fly the Council of Europe flag on Europe Day “as a mark of our continued ties with that body”, adding the Parliament’s flag policy will now be “amended to reflect these decisions”.