Environment Secretary Richard Lochhead has proposed to use the new Regulatory Reform (Scotland) Act 2014 to remove the Ministry of Defence's (MoD) exemption from regulation by the Scottish Environment Protection Agency (Sepa).
The MoD detected low levels of radioactivity emanating from a microscopic breach in a reactor at the Vulcan nuclear submarine test-bed at Dounreay, Caithness, in January 2012.
The reactor was deactivated for 10 months but the Scottish Government were only recently informed.
In a statement to Holyrood, Mr Lochhead said: "We see evidence of the MoD's culture of secrecy and cover-ups when what we need is openness and transparency.
"Sepa's role under the Radioactive Substances Act 1993 is to regulate the keeping and use of radioactive material and the accumulation and disposal of radioactive waste.
"For sites with a nuclear licence, the Office for Nuclear Regulation regulates most activities on site, with Sepa regulating emissions to the environment and waste.
"But Sepa's role on military sites such as Vulcan is different.
"The Act does not apply to premises used for defence purposes, so Sepa has no power to regulate. Basically, the MoD has a Crown exemption from the legislation that applies to everyone else.
"This Parliament has recently passed the Regulatory Reform (Scotland) Act 2014, which allows us to introduce a new consistent, coherent, proportionate and transparent environmental regulation regime for Scotland.
"We want to get rid of anomalies like Crown exemption and treat all those subject to regulation even-handedly.
"We, therefore, propose to use the forthcoming regulations under the Regulatory Reform Act to leave behind the Crown exemption for MoD sites."
Labour environment spokeswoman Claire Baker said it was "completely unacceptable for the UK Government not to have informed the Scottish Government of this episode".
But she said there are "contradictory statements about Sepa's decision not to share information with the Scottish Government".
"Sepa state that the MoD requested a strict need-to-know basis," she said.
"But also they said as radioactive discharges were well below the authorised limit and there was no environmental impact, Sepa did not inform the Scottish Government - which would suggest this was a decision made by Sepa."
Mr Lochhead said: "Sepa are bound by the terms of the agreement about what they can say in terms of the circumstances at the reactor, and that is why if we remove the Crown exemption we will strengthen the hand of Sepa and they will be able to regulate properly. Sepa will call the shots, not the MoD."
Conservative MSP Mary Scanlon suggested the Scottish Government was "scaremongering".
She said: "Given the fact that this event is classed as zero on the International Atomic Energy Agency's measurement scale, why are the Scottish Government scaremongering and raising uncertainty over the 300 highly-skilled, highly-paid jobs at HMS Vulcan in Caithness?"
Liberal Democrat leader Willie Rennie said that strict safety limits had not been breached.
"In raising that matter in the manner that he has, is the minister confident that he has not risked causing unnecessary alarm?" Mr Rennie asked.
Mr Lochhead said: "As the Government and Sepa have said, in terms of the discharges from the plant, they did not breach safe limits.
"However, if Sepa are supposed to be able to do their job properly, they need to understand why the discharge limits were being raised, and for 10 months they were kept in the dark about what was happening at the Vulcan facility."
He went on to add that the episode showed there was a "culture of cover-ups and secrecy" within the MoD.