The quality mark initiative will be launched by industry and energy minister Brian Wilson in Birmingham next Thursday and in Somerset the week after.
The chief executive of the National Federation of Roofing Contractors, Edward Cowan, is one of the critics of the warranty.
He said: "The NFRC is concerned about the problem of the expense that warranties bring within the quality mark scheme.
"Contractors will have to commit to an expense for all domestic work, but are hard businesspeople who will want to see a sufficient return on their investment."
Ian Davis, director-general of the Federation of Master Builders, said his association had created a warranty scheme for the quality mark. However, he added that many members had refused to join because they believed the FMB's existing Masterbond warranty offered better value for money.
The Masterbond warranty does not make federation members eligible for the quality mark scheme.
Davis said: "We do not promote the quality mark to our members, and we have a significant number of members who believe they have been through a formal vetting process and believe that they already have adequate financial protection."
The DTI confirmed this week that 150 firms are signed up to the two pilot schemes – 125 fewer than originally expected.
We do not promote the quality mark to our members
Ian Davis, director general, FMB
Builders are also still sceptical about whether the the government will give the scheme sufficient publicity.
The warranties will cost contractors a minimum of 0.75% of the value of their domestic turnover annually, and will provide cover on a given job for up to six years.
The Heating and Ventilating Contractors Association has announced that it has negotiated its own warranty scheme that meets the government's requirements for the quality mark.
The HVCA has agreed a scheme whereby members have to contribute only 0.5% of their annual domestic turnover to join the scheme, but the figures have only just been sent to members.
A spokesperson said it would be a race against time to convince members to sign up to the scheme.
A DTI spokesperson said the department was aware of the problems surrounding the warranties and said that it hoped that once the scheme was launched and firmly backed, the cost of warranties would fall.
The spokesperson said the DTI was in talks with the FMB to iron out problems surrounding warranties and was fully committed to getting it signed up.