Scotland's Environment Minister, Richard Lochhead, has written to the UK's Under Secretary for Defence, Philip Dunne, saying that waste from dismantling the vessels "should not be stored in Scotland".
Last month, the MoD proposed an old nuclear site at Chapelcross, in Dumfries and Galloway, as a potential store site. But this now looks likely to be dropped as a result of Lochhead's intervention.
That would mean the waste going to one of four sites suggested by the MoD in England: Sellafield nuclear complex in Cumbria; Capenhurst nuclear site in Cheshire; MoD nuclear weapons plants at Aldermaston; and Burghfield in Berkshire.
The MoD has been trying to decide for more than a decade what to do with the seven old subs tied up at Rosyth, as well as 11 at Devonport on the south coast. Its latest plan is to dismantle them at the yards and move the resultant waste elsewhere.
The Sunday Herald revealed in February that taking apart the Rosyth submarines would produce more than 3600 tonnes of radioactive waste. Lower-level wastes will go to the official dump at Drigg near Sellafield, and higher-level wastes are intended for a store at a site yet to be decided.
The proposed store is described as "interim" by the MoD - though designed to last more than 100 years and have the capacity for the waste of nine more vessels still in service. The final aim is to dispose of the waste in an underground repository but no community has agreed to host it.
A Holyrood spokeswoman said: "The Scottish Government has made clear to the MoD this waste should not be stored in Scotland and we will continue to make this case."
Jane Tallents from the Nuclear Submarine Forum, which brings together concerned communities, said: "The UK Government should consider what brings real security for people and stop taking risks and wasting money with nuclear powered submarines."