The release - in which Britain's flag was described as a "butcher's apron" - came from the office of Sandra White, the Nationalist MSP.
But when it became public the MSP insisted the press release did not have her approval.
The party worker who sent it, Mark Hirst, yesterday quit as Ms White's researcher and released correspondence suggesting she had approved the statement on Monday afternoon.
In a statement, Mr Hirst said that because his integrity had been questioned, it was "with considerable regret" that he had to clarify what had happened over the issuing of the press release in Ms White's name.
The e-mail released by Mr Hirst shows that Ms White told him she wanted to hold off tabling a motion at Holyrood condemning Gordon Brown, the Chancellor, for his speech calling for households across Britain to fly the Union flag.
It also shows that she told Mr Hirst to take out the final two paragraphs of the press release - which would have publicised the motion.
However, on the basis of an earlier e-mail in which she said "yes okay" to his first draft, Mr Hirst released the statement to the media. This included a claim that under the shadow of the Union flag "the first concentration camps in history emerged, the first civilian populations in Iraq were gassed, civilian massacres in India and Kenya followed and later again in Derry".
However Mr Hirst's e-mail, released yesterday, showed that Ms White had said the rest of the draft was "good", which effectively approved the sentences: "For almost 300 years, the Union jack, which was commonly referred to as the butcher's apron by most Scots, has been soiled by the actions of successive British governments, not just here in Scotland but throughout the world.
"Under the Union flag our own nation witnesses some of its most serious trauma; the suppression of the clans, the Highland Clearances, the disproportionately heavy losses sustained by Scots in Britain's military adventures, and internationally the Union flag's reputation is little better."
Alex Salmond, the SNP leader, yesterday refused to condemn the language used in the press release. Asked if he supported the comments attributed to Ms White, Mr Salmond said: "She didn't make any comments. That's the point. As I understand it, she didn't table the motion the press release was based on because she didn't agree with comments in the motion.
"There was obviously a breakdown in communications. We accepted that there had been confusion, which was why Mark wasn't disciplined. He decided to resign as a result of that. That's his decision. That's unfortunate, but when a relationship breaks down between an MSP and his or her members of staff, that is an outcome that is likely."
Mr Hirst will continue to work for Christine Grahame, another SNP MSP.
Bill Aitken, the Scottish Conservatives' Holyrood chief whip, said: "While we are reluctant to intrude upon private grief, it is quite clear that even the edited e-mail demonstrates a disturbing and negative attitude on behalf of the SNP."
He added: "Despite all their ducking, weaving and efforts to pass the buck on to one of their employees, this whole matter illustrates to us a party with a blinkered, bigoted anti-Englishness and anti-Britishness which should concern us all."