The local community in Caithness was told there was "little" to report when in fact the site's Vulcan reactor was shut down for several months in 2012, according to Scottish Environment Secretary Richard Lochhead.
Last week, Defence Secretary Philip Hammond revealed that Britain's oldest nuclear submarine, HMS Vanguard, was to have its reactor refuelled at a cost of £120 million after the Vulcan test reactor was found in 2012 to have "low levels of radioactivity ... in a prototype core".
Mr Lochhead, who will make a statement to the Scottish Parliament this afternoon, said the minutes of meetings of the Dounreay Stakeholder Group showed the Ministry's "culture of secrecy just gets deeper and deeper".
He said: "They then told the community it was 'business as usual' when that clearly was not the case given that the Vulcan reactor was shut down for several months in 2012 in response to abnormal levels of radiation within the facility.
"Not only did the Ministry of Defence not inform the people of Scotland, the Scottish Parliament or the Scottish Government of this nuclear-related issue, they actually told the local community there was 'little to report' when clearly there was plenty to report."
Mr Lochhead said the documents showed "what appears to have been a campaign by the MoD to deliberately mislead people over this incident and to cover up the truth".
He called for complete openness on any such nuclear-related incident in Scotland given the potential environmental impact. He added: "It raises the question of whether local stakeholders, or anyone else, can trust what the MoD says."
A Whitehall source, who dismissed the charge of a cover-up as "complete nonsense", accused some in the SNP administration of "commandeering" the issue to further the cause of Scottish independence.
He pointed out how the global nuclear monitoring watchdog, the International Atomic Energy Agency, had classed the incident of two years ago as level zero. "There was no risk at all," stressed the source.
Alex Salmond has already demanded an apology from Prime Minister David Cameron for failing to tell Scottish ministers about the incident. The First Minister said Mr Lochhead's parliamentary statement would focus on "what is to be done to bring the arrogance of the MoD to democratic account".
The Whitehall source stressed that it was the responsibility of the Scottish Environment Protection Agency(Sepa) to inform Scottish Government ministers of any nuclear-related incident. Subsequently, it was Sepa which decided not to inform given there were no safety risks.
The source stressed that it was not the case that the MoD had prevented Sepa from informing Scottish Government ministers; all it did was to point out the information was classified and not too many people should be informed.
"This issue has been commandeered by those looking for an independence vote," he added.
An MoD spokeswoman said: "It is misleading to confuse a planned gaseous discharge - that is well within safe levels - to monitor cooling water, which the Sepa figures relate to, with a leak. The Defence Secretary has been clear that there has been no leak, that workers remain safe and the local community is not at risk."