The cross-party Yes organisation ordered a local group to stop distributing material endorsing the Wings Over Scotland website.
The move followed a complaint by Conservative MSP Alex Johnstone, who was described by Wings Over Scotland as a liar and "fat troughing scum".
The leaflet was produced by Yes Edinburgh North & Leith, which gave its address care of the main Yes Scotland office in Glasgow.
It listed 20 links to pro-independence blogs and websites which, it said, provided "information you won't find on television or in the newspapers".
The list included Wings Over Scotland, which it described as "dissecting arguments, debunking myths".
Wings Over Scotland, produced by Bath-based campaigner Stuart Campbell, is an outspoken site with a cult following among diehard nationalists.
Its often foul-mouthed tweets are followed by nearly 14,000 people.
In a letter to Blair Jenkins, the chief executive of Yes Scotland, Mr Johnstone said: "If describing an MSP as a 'fat, troughing scum' is your idea of a well-made argument or a clever way to debunk myths, then the standard of our national debate really has fallen into disrepair.
"I do not care what Wings Over Scotland says about me or any other pro-Union politician.
"But I do think as a supposedly reputable campaigning organisation, you should immediately condemn this abuse, and remove the link to the website."
Yes Scotland confirmed the local group had been told to stop distributing the leaflet.
A spokesman said: "It was a leaflet produced by a local group in Edinburgh, which provided links to 20 websites for information, and its distribution has now been discontinued.
"Yes Scotland has taken immediate action on this complaint, which is rather more than has been done by the leader of the No campaign, Alistair Darling, who has still not apologised for his intemperate attack comparing Scotland's First Minister to a North Korean dictator."
Wings Over Scotland was at the centre of a furore over Clare Lally, a Labour activist who described herself as an "ordinary mum" during a Better Together rally.
"Wings", as the website is known to its fans, highlighted her links to Labour shortly before Alex Salmond's spin doctor Campbell Gunn passed the information to a newspaper, prompting calls for him to be sacked for allegedly breaching civil service rules.
At the time, both the Scottish Government and Mr Campbell denied they had any contacts with each other.