Mr Darling, who is leading the campaign against Scottish independence, has been accused of co-ordinating the present Conservative-Liberal Democrat-run Treasury's opposition to a currency union.
He was questioned over his links to Permanent Secretary to the Treasury Sir Nicholas Macpherson, who he worked with during Labour's 13 years in government, at Holyrood's Economy Committee.
Yes Scotland has attacked the "suspicious" co-ordination of the UK Treasury, Labour and Better Together in attacking the Scottish Government's plan to keep the pound.
Mr Darling confirmed that he met with Sir Nicholas socially as recently as March, a month after the civil servant publicly advised against a currency union, but refused to reveal what was discussed.
SNP MSP Joan McAlpine quoted a Treasury source in The Guardian newspaper who reportedly said: "Alistair and Andrew are running the show - we just did what they said".
Ms McAlpine said: "They were referring to Andrew Dunlop, the Prime Minister's special adviser for Scotland who also advised Margaret Thatcher and yourself. Can I ask when you and Mr Dunlop first ruled out a currency union?"
Mr Darling said: "We didn't and it's news to me that I am running the show as far as the Treasury was concerned. I did, but I don't now.
"I don't 'run the show'. Of course I have discussed with Ed Balls, George Osborne, Danny Alexander a currency union. It would be extraordinary if I hadn't done so."
Conservative Chancellor George Osborne ruled out a currency union in March, controversially publishing Sir Nicholas's advice in a break from the civil service's convention of confidentiality.
Labour and the Liberal Democrats backed this stance and Better Together published a dossier briefing against a currency union within minutes of the Chancellor's announcement.
Better Together campaign director Blair McDougall told the committee that he had been informed of the Treasury's currency decision "a matter of days before it happened".
Sir Nicholas has said that the Chancellor first saw his advice "a couple of days or 24 hours before", in evidence to the Commons Public Administration Select Committee last month.
The SNP has raised concerns that Better Together was informed about the currency decision before the Chancellor while Yes Scotland has described the timing as "suspicious".
Dennis Canavan, chair of the Yes Scotland advisory board, told the Economy Committee: "I am very suspicious about the timing of all of this and it seems to me rather coincidental - it's too much to say it's simply coincidence that the three spokespersons for the three major political parties at Westminster suddenly came together and said we are ruling out completely any currency union."
Ms McAlpine added: "Better Together published a dossier immediately after Osborne's announcement claiming that a currency union wasn't possible. Had you been told what the UK Government was announcing?"
Mr McDougall said: "In a matter of days before it happened, yes. Not about whether the decision should be made but that a decision was coming."
Mr Darling said: "The actual production and preparation of the Treasury paper that you refer to is obviously a matter for the UK Government because that's what governments do.
"Although the process is fascinating to some, I would have thought what's more interesting is the actual substance of a currency union which I think would be bad for Scotland, never mind the rest of the UK."
Mr Darling said he "bumped into" Sir Nicholas in March but refused to reveal how many times they had met since the start of referendum campaign or what was discussed.
"Obviously I worked very closely with Nick Macpherson for three years and previously when I was Chief Secretary to the Treasury in the late 1990s," he said.
"For the sake of completeness, I also keep up with a number of other permanent secretaries in the departments that I worked and other civil servants. It's not abnormal.
"The one thing I have been very clear on is that every civil servant that I, you know, have contact with are absolutely scrupulous about not discussing what they advise the current government.
"That is one of the strengths of the civil service in this country, so I wouldn't read too much into the fact that, yes, I know Nick Macpherson and I saw him nearly every day of my life for three years during some quite interesting times.
"In terms of Better Together, in terms of the contact we have with the UK Government, that is done through political channels and not through the civil service.
"I discuss many things, I'm not going to go into private conversations with him or anybody else for that matter.
"What I can tell you is in relation to whatever advice he happened to give to the current government I've not discussed that, no."
Yes Scotland chief executive Blair Jenkins accepted that friendships can continue beyond the term of political office.
He told the committee: "I am not sure I can comment a great deal on that, because as he said I do accept there are friendships that go beyond the roles people happen to be in at any given time."