The training body decided not to pump extra money into training charity Building Lives which will close this month.
The decision has raised questions over the latest round of discretionary funding which saw millions handed out to trade associations.
Among the grants was a £20,000 cheque to the Home Builders Federation to train “non-construction workers” like sales and marketing staff.
A total of 21 organisations were given £7.5m in the last round of funding outside the standard training levy.
Trade associations managed to snaffle more than half the cash.
The funding decisions have come under fire from CITB critics including payroll firm Hudson Contracts.
Director Ian Anfield said: “Neither the Industrial Training Act nor the 2015 Levy Order set the criteria for who is eligible for CITB grants.
“Instead it is up to the CITB and the large industry representatives that dominate its board and committees. This provides little opportunity for accountability and scrutiny of the process, and a number of worthwhile projects have gone unfunded as a result.
“On the face of it, Building Lives looks like it could be one of these projects, but this issue highlights a wider problem with the CITB.
“The CITB is granted levy raising powers only because it is able to convince government that it has industry support.
“This so-called industry support derives from an out-dated consultation process that gives disproportionate power to a number of large firms and federations who are invited by the CITB to represent the industry.
“The CITB should be dragged into the 21st century and embrace open, digital consultation techniques to allow everyone to participate in this process, whether they are a multinational firm or a self-employed tradesman.
“The construction industry is resilient and adaptable precisely because of the number of freelancers and SMEs working in it, but with the CITB their voices are not heard over those who can shout the loudest.
“SMEs and the self-employed pay a disproportionate amount of levy, and are frustrated by the hoops they have to jump through if they wish to claim back training grants.
“We are concerned with the recent funding allocations trumpeted by the CITB. They represent £7.6m from the CITB’s £60m flexible a fund.
“It will be giving large chunks of levy-payer’s money to unaccountable federations who don’t make any contribution to the levy themselves.
“These organizations should be self-funding based on the fees of those who chose to join them, rather than syphoning off levy-payer’s money that could be used to fund worthwhile training.
“If the CITB is genuinely committed to hearing the views of the industry, and they are confident that they have industry support, we invite them to listen to the tens of thousands of SMEs and hundreds of thousands of self-employed people who pay their levy and end up also paying for their own training.
“We want to see the CITB go back to basics and focus on providing training for all, from the self-employed upwards. Like the new Apprenticeship Levy, the CITB levy should be used to fund the actual cost of training and nothing else.
Steve Radley, Director of Policy at CITB, said: “Building Lives’ recent funding application unfortunately did not meet our funding criteria, which were agreed with industry last year.
“These criteria are important because they ensure we are investing levy-payers’ money where it is most needed, with the best chance of success.
“The key elements we were looking for are projects which are employer-led, based on evidenced need, and which cannot be funded elsewhere.
“We take a one-to-many approach when making funding decisions, to ensure that the impact of the funding is felt throughout the industry.
“While some projects that receive funding from CITB are led by Federations, many consist of employer-led consortiums.
“Through HBF, we have supported the development of non-site skills, which are in strong demand for homebuilders.”