Mr Murphy, who was hit by eggs on Thursday, claimed the Yes Scotland campaign was organising "mobs" to intimidate him and undecided voters.
The campaign for independence condemned "all forms" of abusive behaviour.
Scottish First Minister Alex Salmond and Prime Minister David Cameron also spoke out against the egg attack.
Mr Murphy, the shadow international development secretary, has been on his 100 Towns in 100 Days tour, on behalf of the Better Together campaign to keep the Union.
After being egged while speaking in Kirkcaldy, Fife, the Scottish MP said he was suspending the tour for 72 hours to take police advice on the safety of continuing.
In the meantime, he also called on "Yes" campaigners to "call off their attack mobs".
Mr Murphy said his claims had been backed up by footage released by Better Together, which the campaign described as a compilation of several 100 Towns in 100 Days events, including dates in Ayr, Motherwell and Glasgow.
In the footage, the MP is seen being loudly jeered by members of the public, some of whom accuse him of being a "traitor", "parasite", "terrorist" and "quisling".
Mr Murphy told the BBC the first 70 dates of his tour had been "good fun" and "passionate", but recently had taken a "sinister turn for the worse".
"In the past 10 days or so, the Yes Scotland campaign has organised mobs to turn up at every meeting that I'm taking part in to try and silence undecided voters and to try and intimidate me," said the Scottish MP, who pointed to evidence on social media sites to support his claims.
"This isn't about people throwing eggs, this is about a mob mentality trying to silence a quiet patriotic majority.
"It won't work. It turns off undecided voters and it embarrasses the vast majority of good, decent 'Yes' campaigners."
The egg incident was witnessed by Allan Crow, editor of the Fife Free Press newspaper, who tweeted that "Yes" supporters had chanted over Mr Murphy as he attempted to speak.
The prime minister, who has been campaigning in Scotland, said people who threw things at politicians had no place in the democratic process.
"I think the responsibility for the people doing these things lies with the people doing these things," said Mr Cameron, who was visiting a Royal Navy supplier in Midlothian.
"I've always thought that it isn't right to throw eggs at people - I had one myself in Cornwall once, it's an interesting experience - and I'm sure other party leaders would take the same view."
The prime minister added: "It's a vigorous debate with lots of argument, there's nothing wrong with a bit of heckling but throwing things isn't necessarily part of the democratic process."
Mr Salmond said people had "every entitlement to peaceful protest", but added: "People shouldn't throw eggs at somebody full stop, that's something that happens in elections.
"I remember John Prescott getting a bit energised about it in a UK election. It shouldn't happen - I don't think it's at the serious end of things - but it shouldn't happen."
The Scottish first minister also recalled a "road rage" incident, in which he said he was tailed by another motorist waving a "No" sign at him, as a "very bad example" of what could happen in political campaigns.
Mr Salmond also said no responsible politician should seek to take advantage of such protests, as he insisted the overwhelming majority of Scots were "enjoying the most invigorating, scintillating, exciting debate in our political history".
He added: "I don't make the death threats from a few daft people I've had an issue, because I know know 99.9% of people in Scotland are enjoying and being energised by a wonderful political debate."
A spokesperson for Yes Scotland said: 'We condemn all forms of abusive, dangerous and offensive behaviour, whether it be Jim Murphy having eggs thrown at him, or Alex Salmond being harassed by a road rage motorist.
"For the most part, the independence debate has been conducted in a responsible, peaceful and enthusiastic manner with only a very small minority on both sides behaving badly.
"The eyes of the world are on Scotland and it is vital that everybody - regardless of which side of the debate they are on - helps to show off Scotland at its best."
The Courier newspaper reported on Wednesday that Mr Murphy had been verbally abused while campaigning on the streets of Dundee and Montrose.
Also on Wednesday, former Prime Minister Gordon Brown had a speech in Dundee interrupted by a pro-independence protestor.
Labour MP Jim Murphy has suspended his Scotland-wide tour ahead of the independence referendum, citing "co-ordinated abuse" from "Yes" voters.