Scottish politicians from different parties have protested that the UK Government did not inform them about the incident at Dounreay, which occurred in January 2012 but was only disclosed to the SNP this week.
They have also queried the fact the Scottish Environment Protection Agency (Sepa) was not told for months and, when it was informed, did not pass the message on.
The MoD has denied preventing Sepa from telling Scottish ministers about the internal leak, which involved a "miniscule" amount of radiation in a test reactor at Dounreay.
The MoD insisted it was the responsibility of Sepa, not the MoD, to inform the Scottish Government about the leak and it added Sepa had made the right decision not to pass on the information, as there had been no safety risks to the community.
An MoD spokesman said: "Sepa themselves chose not to inform ministers based on their expert view that the local community and environment is not at risk."
Labour's shadow Scottish Secretary Margaret Curran has written to Sepa's chief executive Professor James Curran to ask who took the decision not to inform Scottish ministers.
A spokesman for Sepa said: "Sepa has received a letter from Margaret Curran MP and a response will be provided in due course."