The message read "What a #bitch after we gave her shelter in our city when she was a single mum", and was tweeted around 1pm today. It has since been retweeted over 100 times.
The charity, ironically named The Dignity Project, was clearly upset by the Harry Potter creator's decision to donate such a large sum to the campaign, which is run by her friend and former chancellor, Alistair Darling.
However, many tweeters - including Scottish independence supporters - defended the writer and expressed their outrage over the missive, branding it a disgrace.
Comedy writer Simon Blackwell pointed out that they might want to look up the meaning of dignified. Others blasted the charity as being misogynistic, while some suggested that Rowling had done a lot for the country and charity, particularly in light of the fact she donated £10 million in 2010 to the University of Edinburgh's MS research clinic.
Rowling's involvement with the Better Together campaign and her decision to offer such a large donation was announced in a piece on the Guardian earlier today.
The writer made a statement on her website about her donation:
"My hesitance at embracing independence has nothing to do with lack of belief in Scotland's remarkable people or its achievements. The simple truth is that Scotland is subject to the same 21st-century pressures as the rest of the world.
"It must compete in the same global markets, defend itself from the same threats and navigate what still feels like a fragile economic recovery. The more I listen to the yes campaign, the more I worry about its minimisation and even denial of risks."
The charity has yet to respond to criticism on Twitter. Stylist has contacted the Office of the Scottish Charity Regulator and is awaiting a response.
The Dignity Project claims that it has been hacked and is not responsible for the tweet.
A message on their website read:
"The Dignity Project has had it's Twitter account hacked. We are not responsible for any tweets that have been sent. As a charity we do not take any political stance and our opinion is people are free to donate to whoever they choose. To the people who hacked our account if helping African children to thrive and survive including single mums is bad thing that is their problem. "
Not my independence, you bitch!
But seriously though, this is embarrassing.