Environment Minister Ross Finnie has pledged that public safety would be given top priority when dealing with the burial of nuclear waste.
The clean-up of Dounreay is expected to take until 2033
He was responding to an influential committee which has recommended burying nuclear waste deep underground.
The Committee on Radioactive Waste Management also said robust interim storage facilities would be required in the meantime.
Its remit did not cover recommending specific sites for the burial.
However, it said a process had been set out to determine where any facilities should be located, including identifying parts of the UK with suitable geology.
The process leading to the creation of suitable facilities for disposal may take several decades.
The committee also said communities in those areas should then be invited to take part in discussions.
It has been estimated that the UK has enough radioactive waste to fill almost 200 Olympic-sized swimming pools.
Mr Finnie said: "We have no intention of forcing nuclear waste on any community."
He praised the committee's work, saying members had undertaken an extensive programme and had examined all the options.
He added that the report would "provide a strong basis for taking forward a programme to deal with higher level radioactive wastes".
Mr Finnie said public safety is the key concern
The Scottish Executive has always insisted there will be no new nuclear power stations until the issue of waste is resolved.
Mr Finnie said: "Public safety and environmental protection will be our utmost concern in taking forward the programme for the long-term management of the UK's higher activity wastes.
"The government well understands the importance of independent scrutiny on issues of nuclear power.
"We will ensure in taking this programme forward that there is a robust regulatory regime and independent oversight."
However, Nicola Sturgeon, the Scottish National Party's Holyrood leader, said Mr McConnell must publicly state his position on new nuclear power stations.
"He must come off the fence about Scotland's nuclear future," she said.
"He cannot hide from the Scottish public any longer, he must be clear about whether his legacy will condemn Scotland's next generation to a future with additional deadly nuclear waste by supporting the development of new nuclear power stations.
"The people of Scotland do not need, nor do they want, a new generation of nuclear power."
The Scottish Greens called on Mr McConnell to reject the building of new nuclear power stations, arguing instead for greater use of renewable power.
Co-convener Robin Harper said: "It is clear that there is still no solution to the problem of nuclear waste.
"What is needed now is the political willpower to seriously advance renewable energy and energy efficiency."
Nora Radcliffe, the environment spokeswoman for the Liberal Democrats, said: "This report must not be seen as giving a green light to new nuclear build in Scotland.
"This report is dealing with our dangerous radioactive waste legacy, not the separate question of new nuclear build.
"Nuclear power remains unwanted, unsafe and uneconomic."
She added that the Liberal Democrats would focus on improving energy efficiency and investing in renewable energy.
The Scottish Executive said it would give a full response in the autumn.