Alex Salmond has backed yes campaigners who staged an angry protest outside the BBC's Scottish headquarters over perceived bias shown by the corporation's political editor, Nick Robinson.

The National Union of Journalists condemned attempts to intimidate journalists after Sunday's protesters, objecting to what they regard as the BBC's pro-union bias, said Robinson was a liar and called for him to be fired.

Alarmed by the protests, the NUJ has pressed BBC executives in Scotland to step up security with police to protect BBC journalists during voting and the referendum counts on Thursday, as concerns mounted they could be the focus of abuse or intimidation.

Salmond, Scotland's first minister, said he did not want Robinson to be sacked and did not believe he was a liar. But he said the BBC had been unfair and unreasonable in the way it edited a tense exchange between Salmond and Robinson at a press conference on Thursday.

Robinson was accused by the first minister of "heckling" after he pressed Salmond to answer further questions about the threat of Scotland-based banks to move their registered offices to London.

Asked during a press conference at Edinburgh airport whether he supported the protesters' intimidation of journalists, Salmond did not directly answer the question but said: "I think there's real public concern in terms of some of the nature and balance of the coverage.

"We must allow people to express a view in a peaceful and joyous fashion, that's part of the democratic aspects of politics [sic]. … My view of this referendum campaign, if we leave to one side the handful of idiots on either side of the debate, [is that it] has been a joyous empowering campaign; a lesson, a model in the exercise of true democracy. "

BBC sources disclosed that some political reporters have been repeatedly subjected to verbal and online abuse, with one journalist forced to delete 400 abusive tweets from his official Twitter feed. The corporation has defended Robinson's report after it received a flurry of complainants, and insisted it was "balanced and impartial".

Paul Holleran, the NUJ's Scottish regional organiser, said there had been an escalating series of incidents in which journalists in Edinburgh and Aberdeen had been abused when they came to report events by both yes and no campaigns.

"Others were on the receiving end of a range of abuse and intolerance on social media, some of which has been logged and may be reported to the police," Holleran said. "Robust debate is fine. Pointing out when journalists get their facts wrong is expected and welcomed. But NUJ members believe in a free press, a fair media, with journalists allowed to do their jobs free of intimidation.

He added: "What is totally unacceptable is the use of threats of violence."

Branding the protesters a mob, Alistair Carmichael, the Scottish secretary, urged Salmond to call the protests off. "These are serious, serious tactics to be adopted and really, the person who could stop it all and pull the heat out of this is Alex Salmond. But time after time, despite every invitation to do so, he just ignores it," he said.

Nicola Sturgeon, Salmond's deputy, later distanced herself from the BBC protests; the corporation's Scottish headquarters at Pacific Quay fall into her Glasgow Govan constituency. She emphasised it was not organised by the official Yes Scotland campaign but implied the protesters were wasting their time and energy, arguing they should spend the last three days "not protesting against something but campaigning for something".

Asked to clarify his views by reporters about the demands for Robinson to be sacked, Salmond added: "I certainly don't want him to be sacked. I saw the two clips. I don't think it was fair for Nick to suggest that I hadn't answered a question when I actually answered it twice.

"It wasn't reasonable to cut a report in such a way as to imply that the question hadn't been answered." Asked if he thought Robinson was a liar – as stated in a large, full-colour banner used in Sunday's demonstration – he said: "No, I don't."

Salmond also insisted that the Queen had not intervened in the independence debate when she told wellwishers at Crathie kirk on Sunday that she hoped "people will think very carefully about the future" after being asked her thoughts on the referendum.

Her remarks followed reports last week that the Queen was very alarmed about the threat of the UK breaking apart, which were later denied by Buckingham Palace. But her statement on Sunday, which was not disputed by the palace, was interpreted by no campaigners as a sign of her anxieties about independence.

Salmond responded last week by stating he believed the Queen, whom he saw in private in late August at Balmoral, was relaxed about independence. Asked about her remarks on Sunday, Salmond said: "I think that Her Majesty the Queen is absolutely impartial on the referendum. I think that the statement from Buckingham Palace last week made that perfectly clear.

"Her Majesty the Queen as a constitutional monarch is completely impartial on this matter. This has been stated many times; no one except the most frenetic unionist press would seek to persuade or tell people otherwise. I look forward to Her Majesty Queen Elizabeth being Queen of Scots in an independent Scotland."

• This article was amended on 17 September 2014. An earlier version referred to Craithie, rather than Crathie kirk.