Labour MP Jim Murphy was pelted with eggs and said he has been threatened with violence during his 100 Towns in 100 Days tour.
Today, Murphy accepted that Salmond has not personally orchestrated the attacks, but the SNP leader has spoken out to urge Yes supporters to ignore the unionists in future.
"I condemn any egg throwing or any intimidation from any side," Salmond told Sky News' Murnaghan show.
"Somebody was convicted, of course, of online threats against me. Somebody thought his car should be a political weapon. There was a woman, a Yes campaigner, assaulted on the streets of Glasgow.
"I don't hold press conferences accusing Murphy of orchestrating these events, because I know that would be ridiculous to do so.
"So let me be absolutely clear to people watching, if Murphy comes balling and shouting in a street corner near you any time soon keep doing your shopping, keep doing what you were doing.
"He's just like the guy with The End Is Nigh round his neck - he'll go away soon."
Ukip has offered to join Murphy's "wishy washy" tour to "make sure he stays safe" when it comes to Scotland for a pro-Union rally in two weeks.
Salmond urged campaigners to steer clear of Ukip and its leader Nigel Farage, who had to be evacuated from a pub in a police riot van after Radical Independence and anti-Ukip protesters barricaded him inside during a previous visit to Scotland in May 2013.
Salmond said: "If Farage comes in a blaze of publicity in the next few days, as he says he's going to do, ignore him, he will go back to Clacton very soon."
Murphy told Murnaghan: "I don't mind heckles and, d'you know what, I don't even mind people throwing eggs - that's just a dry cleaning bill.
"But what happened after the first televised debate between Alistair Darling and Alex Salmond is that things took a sinister turn.
"Instead of turning up in crowds of people on all sides there was an organised mob of Yes supporters, facilitated through Yes Scotland and local organisations through websites, Facebook and other social media."
The mobs turned over tables, climed on crates and tried "to attack a photographer because they happened to be English", according to Murphy who said he has been called "a traitor, a quisling, a terrorist and much else that I can't say" and challenged to several street fights.
"I'm not suggesting Salmond has orchestrated this, of course I'm not, but Yes Scotland at a local level have made that happen," he said.
Salmond said Murphy was being "absolutely and utterly ridiculous" and urged people to visit a blog by an Aberdeenshire journalism graduate to see "exactly see what Mr Murphy has been up to".
The Still Raining, Still Dreaming blog said No voters shouted, pointed fingers and threatened to take Yes signs off nationalists at a Better Together rally in Stonehaven.
Murphy looked on and denied that both sides of the campaign had intimidating supporters, the blog said.