The losses cast a fresh shadow over the security of the Dounreay site. The Government recently agreed to spend an estimated pounds 400m of taxpayers' money in emptying the dump and storing the recovered material for the long-term in a new facility to be built at site on the north coast of Scotland.
The disclosure that the atomic material had gone missing was made in an inventory of the shaft at the site by the Atomic Energy Authority.
A spokesman for the AEA tried to reassure the public that there was no immediate danger over the losses, which are likely to have occurred in the 1960s.
The AEA spokesman said it could be explained by over-accounting for the amounts of uranium stored, due to the imprecision of the analytical techniques at the time.
Calls for an inquiry were led by the Scottish National Party's environment spokeswoman, Roseanna Cunningham, who called on the Government to launch a South-African style truth commission to determine what happened to the missing uranium.
"How on earth can material as deadly as this just go missing? As usual one gets the feeling that we are not being told the whole story. Either that or Dounreay's incompetence down the years has been even worse than anyone imagined," she said.
Ms Cunningham said the waste shaft at Dounreay had been "a disaster story".
"Whether this latest development reveals deception or simply yet more bungling inefficiency, the consequences are a confusion which is potentially dangerous."
She added: "It is now incumbent on the Government to press the UKAEA for an answer as 'material unaccounted for' is just not good enough. Uncertainty can be lethal in the nuclear industry."
Dounreay said in a statement that the recently-published inventory was prepared to "establish a worst-case estimate" of its contents, and therefore "rightly made pessimistic assumptions about the possible contents of the shaft".
During the 1960s the plant processed material from a wide range of sources, including residues from other UKAEA sites which were difficult to analyse because of their variable nature and composition.
Senior scientists at the complex, headed by Dr Sandy McWhirter, believe that the uranium was either tipped into the waste shaft or remains lodged behind radioactive concrete shields in one of Dounreay's reprocessing plants.Reuse content