The UK Atomic Energy Authority (UKAEA) pled guilty to four charges under the Radioactive Substances Act 1960: one of disposing of radioactive waste at a landfill site at the plant between 1963 and 1975 and three of allowing nuclear fuel particles to be released into the Pentland Firth between 1963 and 1984.
The charges were brought after UKAEAwas reported to the procurator-fiscal following a lengthy investigation by the Scottish Environment Protection Agency (Sepa).
Wick Sheriff Court heard yesterday that fuel fragments which were supposed to be disposed of in a storage shaft had been put in 46,000 cubic metres of landfill. The error came to light in July 1999.
Alasdair MacDonald, procurator-fiscal forCaithness, Sutherland and Easter Ross, said six radioactive particles were removed from the landfill and two from the coast.
He added that such solid radioactive waste could only have legally been disposed of in a low-level pit.
Between December 1963 and December 1984, nuclear particles entered the sea from a drain.
The court heard was told that this drain was supposed to contain only liquid waste, but storage tanks were not properly filtered, allowing contaminated material to escape.
Mr MacDonald told the court that, between 1976 and the end of 2006, 1401 radioactive particles were recovered by UKAEA from the foreshore and nearby Sandside Beach.
He said Sepa had found between 1000 and 4000 particles within 15ft of an overflow pipe at Dounreay.
UKAEA also admitted allowing fragments to escape from two other pipes at the site.
Mr. MacDonald said: "This appears to be a clear unauthorised disposal of solid radioactive waste as a matter of incompetence. It has not only lasting consequences for the future, but provides a clear signpost back to the mistakes of the past. Particles were literally flushed out to sea over a 20-year period."
Mr. MacDonald said four nuclear fragments recovered from Dounreay's foreshore and two from the sea bed were considered "very dangerous" and could be fatal if ingested.
David Stewart, for UKAEA, said it was accepted that a small amount of radioactive material had been found in the landfill site and had been released into the sea. But a study had shown only an extremely small possibility of a member of the public coming into contact with a particle on local beaches.
Sheriff Andrew Berry deferred sentence until February 15.
Dr John Crofts, director of safety with UKAEA, said outside the court: "UKAEA deeply regrets that some particles were released from the site. The practices which gave rise to these particles ceased long ago."
A spokesman for Friends of the Earth Scotland said these incidents illustrate "the idiocy of considering an expansion of nuclear power in Scotland".
Dounreay, a former fast reactor research and development centre, was shut in 1994 and is earmarked for a GBP2.9bn decommissioning by 2033.
Last year UKAEA was fined GBP2m after 266 litres of hazardous, dissolved spent fuel spilled on to a laboratory floor at the plant.