Richard Lochhead will voice concerns Holyrood ministers and the wider public were "kept in the dark" on the issue by the Ministry of Defence (MoD).
He proposes to address the Scottish Parliament tomorrow about the incident at the UK Government's Vulcan Nuclear Reactor Test Establishment at Dounreay, Caithness.
UK Defence Secretary Philip Hammond revealed last week Britain's oldest nuclear submarine, HMS Vanguard, is to have its reactor refuelled at a cost of £120 million after the test reactor was found to have a small internal leak of radiation.
He told the Commons the work was being carried out after "low levels of radioactivity were detected in a prototype core" in 2012.
Mr Hammond said the test reactor had been shut down after the fault was detected and both the independent Defence Nuclear Safety Regulator and the Scottish Environment Protection Agency (Sepa) had been informed.
Mr Lochhead was notified of the situation shortly before Mr Hammond's statement, the Scottish Government has said.
First Minister Alex Salmond has already demanded an apology from Prime Minister David Cameron for failing to tell Scottish ministers about the problem.
In his statement, Mr Lochhead plans to tell the Scottish Parliament of his concerns that the MoD informed both Sepa and the UK Office for Nuclear Regulation that the incident be kept on a strict need-to-know basis for security reasons.
He will further voice concern Mr Hammond informed the Commons there had been no measurable change in radiation discharge, when the environment agencies reported there had been, the Scottish Government said.
Mr Lochhead said: "There must be complete openness and transparency on any nuclear-related incident of this nature.
An MoD spokeswoman said: "The Scottish Environmental Protection Agency was not ordered to withhold information from the Scottish Government."