Energy Secretary Ed Davey is being called on to "overhaul" the way the Energy Companies Obligation (ECO) scheme is administered.
Under the ECO, the "Big Six" energy suppliers are expected to invest around £1bn a year to provide almost 250,000 low-income homes with free A-rated boilers and insulation.
But energy network Futureproof said the scheme was in danger of descending into "chaos" because of the lack of a unified system to oversee the way consumers apply for the ECO, through to how installers are paid for carrying out the work.
Adam Mitchell, a director of Futureproof, said there were many examples of gas heating engineers going unpaid by approved Green Deal providers for jobs they have completed, or finding forms they have submitted for potential boiler replacements being rejected.
"It is all very well the government talking about targets for the ECO and other government carbon reduction initiatives, but the reality is that the way in which it is administered needs to be overhauled," said Mr Mitchell.
"This is a scheme that is supposed to be helping some of our poorest households keep warm and become more energy efficient, while creating significant amounts of work for installers across the UK. But the problem at the moment is that the various parts of the process - consumers, installers, providers and energy companies - are not properly connected and therefore the scheme is in danger of descending into chaos.
"Only by putting in place a totally joined up and transparent system that works for everyone will ECO deliver the results the government hopes that it will."
The ECO is the grant-funded element of the Green Deal and the cost of the boilers is met by the "Big Six" energy suppliers British Gas, E.ON, Scottish Power, Npower, SSE and EDF.