The complaints have come via the government's "mystery shopper" initiative, launched in February as part of a raft of measures aimed at making sure small businesses are able to compete for public sector contracts.
According to the Cabinet Office, 23 cases were submitted in the first three months of the initiative, with 11 leading to immediate changes and a further seven promising future changes. Only five were rejected.
One common complaint was that the assessment criteria used to filter out applicants was biased against SMEs, while some even included minimum turnover and insurance levels for suppliers that restricted SME access.
Andy Brown, BPIF public affairs advisor, said: "Certainly there is a concern we've come across with local authorities that they some of them are over-zealous in the tests they apply for financial viability and we've had suspicions in the past that printers have been rejected because of their size.
"When that happens you tend to get assurances that that's not the case, that the authority is committed to supporting small businesses and that there was something in the accounts - not connected to the turnover - that raised a question mark over their financial viability.
"That can be very difficult to argue against and we've never been able to isolate it as a prejudice against companies with a turnover below a certain level."
Another criticism that will be familiar to many printers was that pre-qualification questionnaires take too long to complete and ask for unnecessary information. One complaint highlighted a leadership training contract tender by Durham Constabulary that required applicants to complete a 38-page PQQ requesting 163 different pieces of information.