The BBC has been challenged to justify remarks by Andrew Marr after he was accused of expressing personal opinions about Scotland's right to join the EU in an interview with Alex Salmond.

The first minister clashed with Marr after the BBC presenter said: "I think it will be quite hard to get back in, I have to say," on his Sunday morning programme, leading to a surge of complaints on social media about BBC bias.

As Marr sought to clarify his remarks, saying said he was reflecting statements from José Manuel Barroso on an independent Scotland's EU membership prospects on his show last month, Salmond asked whether the broadcaster was talking for himself.

Asking Marr to "hold on a minute", an increasingly irritated Salmond asked: "Is that an individual expression or is that an expression of the BBC?"

Marr replied: "No it's not. I've got no views on this, nor does the BBC."

As the two spoke over each other, made worse by a delay on the line, Salmond retorted: "I mistook you there. I thought you were giving your opinion as opposed to President Barroso's opinion."

The Scottish National party's Westminster culture spokesman, Pete Wishart, went on to Twitter to say "there would be consequences" following Marr's interjection, branding the exchange the worst BBC interview on the independence debate. The party has asked the corporation to explain what Marr meant.

But, in a mark of the high degree of political sensitivity around the issue of EU membership, Salmond has stopped short of making a formal complaint, despite long-standing grievances about BBC coverage. His spokeswoman said they were not lodging an official protest.

She said: "The first minister enjoyed the Andrew Marr programme and was able to correct the comments on air, and isn't minded to complain about it." The BBC, she added later, needed to explain its general approach to the referendum.

The convener of the Scottish parliament's culture committee, Stewart Maxwell, said Marr had previously failed to challenge Barroso's comparison between Scotland's status in the EU with Kosovo's repeated difficulties with its membership application. Maxwell said: "Now a presenter offers what appears to be a personal view on an independent Scotland's EU membership. The comments from Andrew Marr appear to be outside the BBC's editorial guidelines, and no amount of backtracking can change that."

Last month Barroso told Marr in an interview on his programme that he thought it would be "extremely difficult, if not impossible" for an independent Scotland to join the EU because of the likely opposition of some existing member states, like Spain.

Asked about this, Salmond said that he was "quite interested" to see that French parliamentarians claimed recently that Barroso was "being influenced by his potential future candidacy for the secretary general of Nato and was sucking up to London in order to advance that process".

Salmond said that he had "no idea" if that allegation was true.

The BBC responded: "Andrew himself made it clear on air that he had not been intending to express a personal opinion or that of the BBC, but was simply putting forward an argument from President Barroso who, as European commission president, has an integral insight within the debate.

"The BBC's coverage of the Scottish referendum debate has been fair and balanced and we will continue to report on the story without fear or favour."