Labour MP Ian Davidson accused the flagship show of bias during an ill-tempered on-air discussion with presenter Isabel Fraser on Tuesday night.
He dismissed her demand for a public apology at the time and yesterday stepped up his attack when it emerged an expert who contradicted him over the legality of Alex Salmond's referendum plans was a self-proclaimed SNP supporter.
However, Andrew Tickell was introduced simply as an Oxford University lawyer without mention of his role as a high-profile Nationalist blogger, who writes online under the pseudonym "Lallands Peat Worrier".
During his interview, he rubbished a report from Westminster's Scottish Affairs Committee – chaired by Mr Davidson – which concluded that Holyrood probably does not have the legal powers to hold an independence referendum.
Last night Glasgow South West MP Mr Davidson – who repeatedly referred to Newsnight Scotland as "Newsnat" – called for an apology from BBC Scotland. He said: "It's outrageous the BBC should act in this way, presenting an SNP activist and blogger as an impartial academic.
"The issue for me is whether Isabel Fraser knew his background. If not, she was incompetent. If so, this was a conspiracy.
"I was clearly being set up by someone for an ambush. Either way I deserve an apology for the way this programme was conducted."
The spat between Mr Davidson and Ms Fraser prompted an outrcy on Twitter.
Most tweeters regarded Mr Davidson's criticism of the corporation as heavy handed.
SNP MSP Sandra White last night repeated her call for Mr Davidson to apologise and for Scottish Labour leader Johann Lamont to discipline the MP.
She said: "Johann Lamont must now must speak up or speak out to demonstrate if they are a party that promotes positive respectful politics or if they are a party stuck in dark ages."
The SNP confirmed they were aware of Mr Tickell's online alter ego when Newsnight Scotland aired but a party spokesman said his affiliations were "not relevant". The spokesman added: "Regardless of whoever else was on the show it was a wild outburst from Ian Davidson. It was his manner as much as anything that has taken people aback."
Labour last night said they were not taking the SNP's calls seriously and indicated Mr Davidson would not be disciplined.
Mr Tickell is a human rights specialist studying for a DPhil at Oxford University's Centre for Socio-Legal Studies. On his Lallands Peat Worrier blog he says he is "a supporter of the Scottish National Party, but who remains distinctly intellectually free floating".
A BBC Scotland spokeswoman said: "We often have contributors on Newsnight Scotland to talk about their area of expertise and add to the debate.
"In Andrew Tickell's case, this is constitutional law."