The abusive Twitter message was posted after Rowling stated her support for a No vote in the Scottish independence referendum with a £1m donation to Better Together and a blog detailing the “serious risks” of independence.
The Harry Potter author, who lives in Edinburgh, has written about her views on her website, highlighting her concerns about the economy and medical research.
Her donation is by far the biggest yet for the pro-union campaign, while Yes Scotland has benefited from £2.5m from Colin and Chris Weir, who won £161m in the EuroMillions lottery in 2011.
Writing in her blog, Rowling said that, while she is “no fan of the current Westminster government”, she has concerns about the economic risks of independence.
“My hesitance at embracing independence has nothing to do with lack of belief in Scotland’s remarkable people or its achievements,” she wrote.
“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 author was born in the West Country, but has lived in Scotland for 21 years.
Criticism quickly flooded in on Twitter, with one tweet from Edinburgh-based charity the Dignity Project reading: “What a #bitch after we gave her shelter in our city when she was a single mum.”
The charity’s post was just one of a number of abusive messages posted by online nationalists angered by Rowling’s public support of the pro-UK Better Together campaign.
She was variously described as a “Union cow bag” and a “disgrace” in social media messages.
Charity regulators said they were making “urgent inquiries” into the matter and seeking clarification from The Dignity Project’s trustees.
Shadow Scottish Secretary Margaret Curran welcomed Ms Rowling’s stance on independence and criticised the “vile abuse”.