The DTI is carrying out a review of the quality mark pilots to decide whether to introduce the scheme nationally.
A source at one trade federation said unless the cost of the accreditation was lowered, contractors would not join. This in turn would lead to trade bodies withdrawing their support from the scheme.
Ian Davis, director general of the Federation of Master Builders, said there was growing concern about the cost of external accreditation.
The trade bodies are also understood to be annoyed that the scheme was extended to Leicestershire and Dover before the success of pilots in Birmingham and Somerset was assessed.
National Federation of Builders deputy chief executive Barry Stephens questioned whether it was necessary to renew membership of the scheme annually. He claimed it would be possible to reduce the costs by auditing firms less often.
Robert Higgs, director of the Heating and Ventilating Contractors Association, also added to the criticism, saying his body wanted develop its own form of accreditation. He added that if the DTI insisted on having an external accreditation and rejected its tests, it would ask members if it should still support the quality mark.
A DTI spokesperson defended the initiative.
He said: "There are a lot of reputable trade associations supporting the quality mark scheme that are recognising its business benefits."
A report outlining the conclusions of a DTI review of the scheme will be sent to construction minister Brian Wilson next month.
It is understood that the DTI is considering merging the quality mark with its other vetting scheme, Constructionline, in an attempt to reduce costs.
The DTI said the idea of a "dual passport" would give firms a two-for-one deal.
The National Federation of Builders and the Federation of Master Builders supported the move. NFB deputy chief executive Barry Stephens said: "The NFB believes that a single list register that reduces cost must be an ultimate objective."