Alistair Darling, the former Labour Chancellor and head of Better Together, had complained on Monday about the "huge disparity" in spending between the two sides in the referendum.
He pointed to big donors backing the Yes campaign and said the Scottish Government was using taxpayers' money to promote the White Paper.
The Scottish Government has said that producing, delivering and promoting the 650-page document has already cost £1.25 million in taxpayers' cash.
Mr Darling said spending so much "simply wasn't right."
However, it has emerged that Whitehall has been spurning Freedom of Information [FoI] requests on how much is being spent on work by civil servants in London on material favourable to the Better Together cause.
It was claimed yesterday that an FoI request was turned down on the grounds of cost.
The SNP has also been refused requests in terms of Westminster Parliamentary Questions on the costs of commissioning evidence helpful to the No campaign.
The SNP made a request for the costs associated with the Scotland Analysis series, a programme of weighty documents produced jointly by the Scotland Office and the Treasury.
It prompted the response: "It is the opinion of a Cabinet Office Minister that disclosing this information would be likely to inhibit the free and frank provision of advice by officials, and exchange of views between officials and could prejudice the effective conduct of public affairs."
A strand of argument has emerged involving scrutiny of top civil servants.
Scotland's chief mandarin Sir Peter Housden has been accused by pro-Union critics of going native and being unduly political in support of the SNP Government.
First Minister Alex Salmond has been strongly supportive of Sir Peter, saying his job is to support the policies of the elected Government at Holyrood.
Treasury Permanent Secretary Sir Nicholas MacPherson has also been dragged into the controversy as it was his advice to George Osborne which was cited when the Chancellor announced that the use of Sterling by an independent Scotland had been ruled out.
Academics have noted that the constitutional debate has put its strains on the tradition of Civil Service neutrality.
Of the claim spending money promoting its White Paper was not legitimate, a Scottish Government source said: "Alistair Darling's bleating can't hide the fact Westminster is spending taxpayers' money on its numerous papers attacking independence and aiding the No campaign - and, unlike the Scottish government, they have thrown up a wall of secrecy around this expenditure."
A Scotland Office spokesman said: "The Scotland Analysis papers are serious pieces of evidence-based work which have been produced to inform the public and help them to make an informed choice in September.
"This work has been carried out within existing teams and from existing budgets. Some costs have been incurred in terms of printing the documents."
Yes Scotland said Alistair Darling's problem was not a lack of money, and that it was being out-campaigned by the grass-roots Yes movement.