The figures show that 38.4% of emissions have been cut since 1990, with levels falling 14% between between 2012 and 2013.
The UK has reduced 27.4% between 1990 and 2013.
Scotland is now over three quarters of the way towards achieving its target of a 42% reduction in greenhouse gases by 2020.
Climate Change Minister Aileen McLeod said: "Scotland is well on track to meet our ambitious emissions targets, with these latest figures for 2013 showing we are more than three quarters of the way there with seven years still to go.
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"Our emissions have fallen by 38.4 per cent from the 1990 baseline, outperforming the original 31.7 per cent reduction that was required to meet the 2013 annual fixed target."
Since the fixed annual targets were set, the baseline has been increased by 10.6 MtCO2e due to changes in the way carbon emissions are measured.
Scotland therefore missed out on its 2013 target by 1.7 MtCO2e.
Ms McLeod added: "Today’s figures show that if it had not been for successive increases to the baseline since the targets were established, Scotland would have met, and exceeded, our target for this year - and the three previous years too."
(LM/MH)
