Many of those questioned said local authorities and enterprise companies have done little to help them develop.
Nearly half of Scotland's workers are employed by companies with less than 50 staff - but according to the federation even more people could be working for such firms.
It is now calling on local authorities and the country's enterprise companies to enter into discussions with small firms to find out how they can give greater assistance.
'Poor service'
Almost two thirds of members claimed that local authorities had done nothing to help the development of their business - and more than a third gave a bad rating for the services provided by their council.
Many also criticised the Scottish Enterprise network but they had other worries too, including education and training.
Four out of 10 respondents thought new employees were not joining their business with the required level of literacy skills.
The findings come from a questionnaire which was sent out to the FSB's 12,334 Scottish members.
Just under 2,000 replies were returned and analysed.
The full findings have now been sent to the Scottish Executive, the Scottish Parliament, local authorities, Scottish Enterprise, representatives of the Scottish education system and the UK and European parliaments.
The Federation of Small Businesses
Scottish Executive
Scottish Parliament
Scottish Enterprise
The BBC is not responsible for the content of external internet sites.
Toys withdrawn in E.coli health scare
Collins calls it a day for Scots
(From Sport)
Pro-lifers plan shock launch
Death inquiry anaesthetist barred
Bowled over by Lord's
Ministers loosen purse strings
'Delight' at Tunnel court outcome
Derby double swoop fails
(From Sport)
Demands for far-reaching information bill
Gaelic makes sound use of the internet
Trusts 'ignoring' depression advice
BBC Scotland - On Air
'Little change' since poverty pledge
Nine hurt as bus crashes into pub
Teachers' union in pay body challenge
Dental death hearing adjourned
Parliament ponders Royal High flit
Reid quits PR job
Industry misses new trains target
Football and royalty dominate Westminster
The next Battle of Britain
(From Sport)
Man charged with murdering lab technician
Lockerbie trial judges named
Festival award for Ratcatcher