In 2012, Mr Netanyahu said Iran needed to be stopped, telling the UN the country could build a weapon next year.
But a Mossad report said Iran was "not performing the activity necessary to produce weapons", according to al-Jazeera and The Guardian.
An Israeli official said there was "no discrepancy" between the accounts.
The Mossad report is part of a batch of documents leaked to al-Jazeera and shared with the Guardian.
They mainly involve exchanges between South Africa's intelligence agency and its foreign counterparts.
Other cables suggest:
The CIA tried to access the Palestinian Islamist group Hamas through backchannels, despite an official ban on contact
South Africa monitored suspected Iranian agents under pressure from the US British intelligence asked for help from the South Africans to recruit a North Korean spy
'Red line'
In September 2012, Mr Netanyahu addressed UN delegates carrying a sketch of a bomb.He called for the world to draw a "clear red line" over Iran's nuclear programme to make it back down.
But in the report, dated 22 October 2012, Mossad appears to take a different view.
While Iran had accumulated some lower grade enriched uranium, "it does not appear to be ready to enrich it to higher levels", the agency says, which would be required for a nuclear weapon.
"Bottom line: though Iran at this stage is not performing the activity necessary to produce weapons, it is working to close gaps in areas that appear legitimate such as enrichment, reactors, which will reduce the time required to produce weapons from the time the instruction is actually given."
Mr Netanyahu and Mossad have reportedly disagreed over Iran in the past.
The leak comes as Iran and six international powers try to reach deal over Iran's nuclear programme, which Tehran insists is peaceful.
