A survey of 200 small firms, conducted by the Centre for Economic and Business Research for the FSB, found 41% of those that sought finance from high street banks in the second quarter of 2012 were refused the cash.
The FSB warned there is an even greater need for greater competition in the Scottish small business finance market because Royal Bank of Scotland and Lloyds Banking Group dominate the sector.
Nevertheless, Scottish businesses are more confident about their prospects than businesses in seven of the 12 other UK areas surveyed, including London, Wales and Northern Ireland.
Andy Willox, the FSB's Scottish policy convener, said: "The FSB has long argued that without more flexible, affordable finance provided by a wider range of players, any hopes of a sustained Scottish recovery will remain some way off.
"The will of small businesses to grow is there, but the money to enable them to do so seems elusive."
There are some signs policy- makers are coming to accept small businesses' complaints.
Last week the Bank of England revealed plans to pump a minimum of £5 billion every month into the banks in the form of six-month loans to kick-start mortgage and small business lending.
A weekend report said this has been boosted by the Bank's decision to allow institutions to release cash reserves to lend out to companies and households.