The request to the Scottish Environment Protection Agency (Sepa) came as it was passed the details from the Ministry of Defence (MoD) in 2012.
The SNP has accused the UK Government of a lack of respect after it emerged that it was not told about the incident at Dounreay for two years.
The MoD had earlier insisted that it had not "ordered" Sepa to withhold information from the Scottish Government.
"Having been told about the situation, Sepa themselves chose not to inform ministers based on their expert view that the local community and environment is not at risk," a spokesman said.
Last night, in response to questions from Labour, Sepa said that the MoD had requested that problems with a test reactor "be kept on a need to know basis".
It added: "Sepa would make a report to Scottish Government in the event of a breach of thresholds or if a need arose to alter discharge limits. As neither of these things occurred and there was no environmental incident, there was nothing for Sepa to report to Scottish Government."
An MoD source said: "We categorically never asked Sepa not to tell Scottish ministers."
He added that the information was given on a "need to know" basis and that it was up to Sepa to determine if Scottish ministers needed to know, adding: "That was their decision. We could not get in the way of that."