The stores, being built at a total cost of £100m, will store tonnes of material from Dounreay nuclear power plant.
This will include items that have been contaminated by radioactivity at the experimental nuclear power complex, such as paper, rags, clothing, glass and concrete.
Workers are excavating 200,000 cubic metres of rock in preparation for pouring a "tank-like" concrete structure, where walls are more than a metre thick.
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A separate encapsulation plant next to the stores will grout the waste into containers, compact drums that will be stored in the larger of the holes.
The stores are separated by nine metres of rock and a complex drainage system has been designed in conjunction with the Scottish Environment Protection Agency.
The contents of the stores will be monitored for 300 years, by which time its radioactivity will have decayed by 95%.
Dounreay is being demolished sixty years after it was built, and the site is being cleaned up.
A spokesman for Dounreay Site Restoration Limited said: "It's the culmination of ten years of work, but the low level waste facility project team can finally see the results of their labours. As the site is cleaned up and demolished, more and more of Dounreay will end up in the vaults."
(NE/GK)
