The Local Data Company (LDC) which compiled the figures said the vacancy rate during the period increased by 1.3% to 16.7% - more than 2% higher than the average across the UK.
All Scottish cities apart from Aberdeen and Stirling saw an increase in the number of empty shops.
Paisley has more empty shops than anywhere else.
The figures, released ahead of Scotland's Towns Conference in Perth, suggest vacancy rates in shopping centres, at 17.9%, are higher than in high streets, at 16.7%, and in retail parks, at 9.1%.
However, the LDC said although the number of empty shops was rising, the "negative trends of 2011 have slowed".
Matthew Hopkinson, director of the LDC, said: "Scotland's retail centres are under the same national pressures of weak consumer spend and the decline of multiple retailer shop numbers.
"As with the rest of UK, independent retailers have remained positive in their growth rates and the multiple closures have slowed but still remain negative."
In the first half of 2012, the number of independent retailers in Scotland increased by 2.3% while the multiple retailers declined by 0.48%.
Professor Leigh Sparks, from the Institute for Retail Studies at Stirling University, commented: "We need data on retail change in town centres and we need regular reporting of activity.
"We need town centres and those interested in them, to recognise this need and act on it."
The Scottish government announced earlier this month that it was reviewing town centres to "scope out" potential solutions to the issues facing them.
The number of empty shops in Scotland has increased in the first half of this year, according to a new report.