During a session of the Public Administration Committee, examining impartiality and the role of the civil service during the independence referendum, Mr Flynn focused on the controversial publication of a memo by Sir Nicholas Macpherson, the Treasury's top civil servant, arguing against a currency union.
Mr Flynn, who represents Newport West in South Wales, said there was an "axis of opposition" to Scottish independence from the English Establishment.
Sir Bob Kerslake, head of the UK Civil Service, said: "Nicholas MacPherson did not align himself on the issue of the referendum. What he did was to make known publicly his advice on the issue of currency. He thought this was a sufficiently important issue to publish his advice."
Sir Bob stressed that such advice was only published when circumstances were deemed "exceptional".
But Mr Flynn said the advice had come down conveniently on the anti-independence side. "Isn't this an example of someone being in breach of the civil service code for impartiality?"
Sir Bob strongly denied this and said Sir Nicholas was advising on what options a government should take on the currency.
After Mr Flynn then turned his fire on what he branded Sir Bob's "sycophantic" article in praise of Margaret Thatcher, Bernard Jenkin, the Conservative committee chairman, sought to call another MP but Mr Flynn tried to continue his line of questioning.
As Mr Jenkin called "order", the Labour backbencher said: "You are using this committee as a stunt to try to embarrass the Scottish Parliament and the idea of devolution." Moments later the Labour backbencher left.