But it prompted claims that the Scottish Government is more focused on "playing to the gallery" on constitutional issues than schools and hospitals.
The controversial decision to stop flying the flag on Friday, when the UK leaves the EU, was made a fortnight ago by Holyrood's corporate body. But it prompted a backlash from the Scottish Government which has been pushing for a rethink.
A vote will be staged after a debate on the issue at Holyrood tomorrow on a motion brought by the Scottish Government which would see the European flag continuing to fly.
The flag is "a symbol of membership of the family of European nations" and Brexit will not change this, according to the Government motion.
It adds that Parliament "recognises the importance of continuing to fly the European flag as a sign of support and solidarity with those EU nationals who have made Scotland their home, and directs and the Scottish Parliamentary Corporate Body to ensure that the European flag continues to fly daily at the Parliament building."
It appears that the SNP and Greens will have a majority at Holyrood which would allow the flag to keep flying.
Holyrood's Presiding Officer Ken Macintosh chairs the Scottish Parliament corporate body (SPCB), which also includes Labour's David Stewart, Liam McArthur of the Liberal Democrats, Andy Wightman of the Greens, the SNP's Sandra White and Conservative Ruth Davidson.
Mr Macintosh today defended the corporate body in a letter to the Government.
The SPCB’s decision-making is neither politically motivated nor reflective of any partial viewpoint," it states.
"Its members serve as parliamentarians, not as representatives of the political parties.
"We discussed the Scotland Act and the powers of the Parliament to direct the SPCB. It is entirely right and proper that the Parliament should have that power, but there was a clear desire from all members of the SPCB today that our flag flying policy should not become a political issue for debate on the floor of the chamber.
"The corporate body recognises entirely the sensitivity that remains over Europe, but its decision is not a political one. Our flags reflect our relationships in law."
Tory chief whip Maurice Golden said the SNP is revealing its "true priorities" by forcing debates in Holyrood this week on flags and independence.
“Valuable time in the Scottish Parliament should be used to address the very severe problems in our hospitals or the crisis engulfing our education system," he said.
“Instead, the nationalists want to revert to the only subject they excel in – stoking up constitutional division.
“It’s completely ridiculous that the governing party of Scotland is dominating business like this on two matters which have already been decisively resolved.
“But for them this isn’t about improving Scotland’s economy or public services, or even enhancing the prospects of the population. It’s about playing to the independence gallery, and trying to cause a ruckus between Scotland and England in the hope it pushes up support for separation.”