The inconsistency was revealed in a cache of communications between South African intelligence services and their global partners -- including Israel's Mossad and America's CIA -- that were leaked to Qatar-based news network Al-Jazeera and Britain's The Guardian daily.
In 2012 Netanyahu told world leaders at the United Nations that Iran could create a nuclear weapon within a year, brandishing a diagram in the form of a lit bomb to indicate the advanced state of Tehran's development effort.
He warned the world that unless Iran was stopped, as of mid-2013 it would only need "a few months, or even a few weeks" of additional uranium enrichment activity to develop a bomb.
But weeks after the speech, Mossad shared a report with South African intelligence which concluded Iran was "not performing the activity necessary to produce weapons," according to the Guardian.
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The discrepancy, the paper said, "highlights the gulf between the public claims and rhetoric of top Israeli politicians and the assessments of Israel's military and intelligence establishment."
The revelations come at a politically sensitive moment as the United States, China, Russia, Britain, France and Germany face a March 31 deadline to reach a deal with Iran to limit its nuclear programme in return for an easing of economic sanctions.
Iran denies seeking an atomic bomb, insisting that its nuclear programme is purely for peaceful energy purposes.
An Israeli government official told the Guardian that there was no contradiction between Netanyahu's statements and the report, claiming both state Iran was enriching uranium to produce weapons.
The leaked documents dating from 2006 to late 2014 consist mainly of communications between South Africa's intelligence agency and other agencies around the world, such as Britain's MI6, Russian intelligence and the CIA.