The three main opposition parties at Holyrood said they suspected so-called "cyber-Nats" had used the cloak of anonymity to send in thousands of submissions favourable to the First Minister's position and bolstering the call for a devo-max question on the ballot paper.
The SNP leadership swiftly hit back, insisting the allegation of rigging was "disgusting" and "absolutely false". It raised suspicions that half of the 3000 submissions to the UK Government's independence consultation were from the Labour Party.
Yesterday, it was also revealed that 70% of respondents to the UK Government consultation agreed with its date of 2013 for an independence poll rather than Mr Salmond's date of 2014.
The rigging allegation first came from Scottish Labour, which urged the SNP Government to "rip up its referendum consultation and start again".
Anas Sarwar, deputy leader of Scottish Labour, said: "Everyone knows that Alex Salmond desperately wants a second question on the ballot and now he has left the door open for his army of cyber-Nats to deliver the response he wants.
"By essentially inviting people to send multiple responses, Alex Salmond has done nothing to dispel the notion that he is trying to rig the referendum."
The Glasgow MP claimed the SNP Government's process was not only "open to abuse, but designed for abuse", insisting: "The idea that people can put in anonymous responses as many times as they like is an unprecedented distortion of democracy. This flawed consultation should be abandoned now."
Stewart Hosie, the SNP's Treasury spokesman at Westminster, responded: "This is absurd in the extreme from the British Labour Party. The rules being used are exactly the same rules as have been used in every single consultation ever.
"If there are questions over the efficacy of any consultation, it should be over the UK one if we find it was so self-selecting that perhaps half the response came from members of one particular party."
Mr Hosie insisted Scots could have confidence in the Scottish Government's consultation, as it would be independently verified, although he did not say by whom. The Dundee MP branded the charge of rigging "absolutely false ... and an appalling accusation."
He added: "I find it disgusting that the good people of Scotland who are entering honestly and openly into this consultation are being put down, talked down and having their entries minimised and diminished in such a crass way by the Labour Party."
Mr Salmond said the SNP Government consultation, which runs until May 11, has attracted more than 10,000 submissions.
Mr Sarwar said claims that the Scottish Government's consultation was the same as others was not true and that people who made submissions to Labour had to put down an email address, while multiple responses were not allowed.
Jackson Carlaw, deputy leader of the Scottish Conservatives, said claims that thousands had participated in the SNP Government's consultation were "risible".
He added: "Nothing the SNP now assert on the basis of a rigged consultation, to which SNP members can contribute anonymously and as many times as they like, will command confidence."
Willie Rennie, leader of the Scottish Liberal Democrats, said: "The Scottish Government needs to publish how many anonymous submissions have been made so we know the scale of the problem."
Meantime Scottish Secretary Michael Moore said 70% of the 3000 respondents to the UK Government's consultation supported holding the referendum sooner rather than later.
He said only 22% of respondents to the consultation, which closed on March 9, supported the SNP timetable of autumn 2014.
"Individual responses showed that Scottish citizens want this issue resolved quickly," he said. "Business responses show the strength of feeling that uncertainty is bad for investors."
A Scottish Government spokesman said: "It is simply not for the UK Government to dictate the legislative timetable of the Scottish Parliament or the terms of the referendum."
Earlier more controversy was caused when footage emerged of Peter Cruddas, the former Conservative Party co-treasurer, saying the Tories needed to be seen fighting for the Union "even if we don't agree with it".
He was reported as saying: "If the Scots say we're out of here and they want to go independent, we can turn around and say it's not what we wanted, it's not what we campaigned for - and you can get on with it."
Deputy First Minister Nicola Sturgeon branded the revelation a "bombshell" for Scottish Tories
A Scottish Conservative Party spokesman said: "The Prime Minister has always been very clear that he wants to keep the Union together."