The number of people in work also increased, with a rise in employment of 4,000 over the three months from May to July to a total of 2,490,000. As a result the employment rate increased slightly, to 71.4%, which is just above the average for the UK as a whole.
Scottish Secretary Michael Moore said the figures "show the scale of the challenge we face in these difficult economic conditions".
He added: "Any fall in the number of people working in Scotland is a serious issue and has a critical impact on the households and individuals affected. That is why we are taking decisive steps to get the economy back into growth and people into work. Creating new employment is something which needs the full focus of both of Scotland's governments and we must work together to achieve it."
Meanwhile, Scottish Finance Secretary John Swinney highlighted the rising employment rate, saying: "The employment rate in Scotland has continued to climb and for the 22nd consecutive monthly statistics release remains higher than the UK rate."
The Scottish Government has repeatedly called on Westminster to release more funds for capital investment in a bid to boost the economy.