The payments of £150 to about 130,000 small businesses were promised as incentives for filing annual PAYE returns online.
However, HM Revenue & Customs (HMRC) has admitted it could take until December to issue the cheques.
The scheme, introduced in 2004, was meant to encourage small businesses to use the online system before it becomes compulsory in 2010. FSB national taxation chairman Bill Knox said: "What we're saying is don't wave a carrot to small businesses if it's going to be left in the air for months. The government quite rightly disapproves of late payment of both tax demands and monies between businesses. HMRC, as an arm of the government, should set an example and pay within 30 days."