Radioactive particles have been traced in the sea and the shore
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Dounreay's boss has warned that new problems at the site may be uncovered as workers enter parts of the complex where no-one has set foot for 50 years.
The former centre of nuclear fast reactor research in Caithness is being decommissioned at a cost of �2.9bn.
Norman Harrison, acting chief operating officer, said the problems will stem from old practices at the site.
He delivered his warning during a speech at the annual prize-giving of the North Highland College in Thurso.
Mr Harrison praised the role played by workers in the clean-up of Dounreay.
Metallic fragments
However, he said the legacies left behind have given staff difficult problems to deal with and was in doubt more will be uncovered as they go further into the site.
The college's new role in training engineers and scientists will help in tackling these issues, said Mr Harrison.
Dounreay has been dogged by the discoveries of radioactive particles on the shore near the site.
The metallic fragments of reprocessed reactor fuel are linked to a rogue historic discharge from the plant.