In his Senate tesimony yesterday, Richard Goss, Director of the CIA, claimed that "There is sufficient material unaccounted for [in Russia], so that it would be possible for those with know-how to construct a nuclear weapon." ABC News also quoted an unnamed "former top official at the Department of Energy" as saying that the reason all this material is unaccounted for is that neither the Soviet Union nor Russia "ever adopted a "mass balance" inventory system that tracks how much nuclear material is produced and where it ends up being used."
All this is highly misleading. The way the "mass balance" system works is that it compares the amount of plutonium at the input and output of the Purex process. Any discrepancy is the "material unaccounted for" or MUF. The problem with MUF is that because of inherent uncertainties of irradiation and inevitable measurement errors this value is never zero. Moreover, it is never an absolutely accurate value either, which may leave enough room for an undetected loss or diversion of plutonium.
In his article on the problems with building a proliferation-resistant reprocessing plant, Marvin Miller concludes that an amount of plutonium that can be diverted from a plant that handles about 7 tonnes of Pu a year cannot be much lower than 3 kg/year even if inspectors employ near-real-time monitoring techniques. We can take this number as an estimate of the "material that cannot be accounted for" due to inherent uncertainty of the plutonium production process. Even operators with full access to the facility and best accounting practices cannot rule out that some material is still lost in the process. There is no reason to believe that just by adopting some "mass balance inventory system" one could account for all the material.
It is true that the uncertainty is fairly small - on the order of 0.05%. However, given the insane amounts of plutonium that the United States and the Soviet Union produced - about 145 tonnes in Russia and about 100 tonnes in the United States - there might be as much as 120 kg of unaccounted plutonium out there - more than enough for a few bombs. This, however, has nothing to do with accounting practices.