Richard Willmott, UK managing director of FAST corporate services, called the BSA's annual software audit campaign "unprofessional".
He told FAST's 2,500 members: "If you receive a letter from the BSA, throw it in the bin and make sure your house is in order."
FAST members include the majority of FTSE 100 companies, a third of public sector organisations and 30 police forces.
The Business Software Alliance is a private company set up by software vendors, including Microsoft, Symantec, Adobe, Corel, Autodesk and Macromedia, to stamp out software piracy and recoup lost revenue for its members.
As part of its current campaign, the BSA has sent out an "annual software audit return " to every UK organisation with 20 or more employees, asking them to conduct a software survey.
However, many users feel that the BSA uses the information provided to demand punitive fines from companies who cannot prove they hold valid licences. The organisation threatens to revoke all software licences, should the offending companies refuse to comply.
Willmott believes that the majority of the fines paid to the BSA come from companies that have volunteered information.
FAST, which was created in 1984 as the lobbying arm of the British Computer Society (BCS), has worked extensively with customs and excise, trading standards and copyright groups promoting training and certification to help companies avoid licensing problems.
"We agree with the BSA in one area. We need to stop software piracy and we go all out against companies that are deliberately using unlicensed software or distributing pirated software," said Willmott. "What we don't do is persecute companies who have lost control of their systems or have strayed. Our job is to help them get compliant and bring in controls to keep them operating within the law."
FAST is concerned at the BSA's name-and-shame policies that last month culminated in 10 companies paying fines on software licence infringements. He also believes that the BSA policy of offering rewards could lead to malicious complaints by disgruntled employees.
The financial and IT consultancy, Mazars, which provides auditing services to FAST members, is also advising UK businesses to steer clear of the BSA.
Ken Shoults, lead IT consultant said: "We have a number of clients who are worried about the methods of the BSA and our advice is to simply to ignore the letters. They are creating a fear that companies who want to tackle the problem of unlicensed software will get railroaded and this is not helpful. "
BSA spokesmen Mike Newton stated that the BSA acts entirely within the law, but would not comment on FAST's warning to its members.