Mr Atherton was participating in a round table discussion on Scotland's renewable energy targets on 7 December 2011.
The government wants renewable sources to generate the equivalent of 100% of Scotland's gross annual electricity consumption by 2020, with an interim milestone of 31 per cent by 2011.
It also wants renewables sources to provide the equivalent of 11 per cent of Scotland's heat demand by 2020.
Citigroup had urged extreme caution over investing in Scotland's renewable energy sector, partly because of the independence referendum, in a recent report.
The major finance group said the referendum process would create huge uncertainty at the moment when major decisions on green projects are needed.
Mr Atherton told MSPs: "To suggest that Scotland having a referendum on whether it stays in the United Kingdom or not carries no uncertainty or risk for particular sectors is preposterous."
SNP MSP Chic Brodie asked why major companies were still investing in Scotland, but Mr Atherton said he could not speak for those companies.
The Citigroup analyst later said in reference to the renewables targets: "I think the industry is planning to fail".
He added it would take a "staggering increase in the investment rates" for the Scottigh government targets to be met.
However Niall Stuart from Scottish Renewables said there were more than enough industry plans to make 100% target, describing it as "ambitious but achievable".
Also taking part in the round table discussion were Professor Paul Mitchell from Aberdeen University; Dan Finch from Moray Offshore Renewables Ltd and David Cunningham from Altium Securities.
They were joined by Colin Ormiston from Vattenfall Wind Power Ltd; Joe Philips from Garrad Haasan & Partners Ltd; Helen McDade from the John Muir Trust; Professor Ian Arbon from the Institution of Mechanical Engineers and Felix Wright from Community Energy Scotland.
In the first part of the committee the Energy minister, Fergus Ewing outlined new regulations referring to Carbon Capture and Storage (CCS).
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