The UK Government's flagship back-to-work scheme has been described as a "miserable failure" amid claims it has been less successful than doing nothing at all.

Official figures show that just 3.5% of those who took part found long- term employment through the Work Programme. However, estimates suggest 5% would have found jobs anyway – without intervention. The Coalition yesterday defended the scheme and said it had no intention of cancelling the scheme. But it has sent notices to a number of the organisations involved in the scheme demanding details of how they plan to improve.

In Scotland, the scheme has helped just 3300 people into a job that has lasted more than six months.

In Dundee, 3470 people were referred to the scheme but just 50 – 1.44% – secured work lasting more than six months.

In Edinburgh and Glasgow the figures were 300 jobs for 6500 referrals and 730 jobs for 16,630 referrals respectively, or 4.6% and 4.4%.

Labour also accused the Tory-LibDem Coalition of massaging the figures to make them look better. The 3.5% figure covers the 14 months to July 2012. However, Labour said in the first 12 months, it had a success rate of just 2.3%.

Ministers said they were prepared to pay up to £14,000 to successfully help the long-term unemployed get back into jobs at the scheme's launch.

They faced accusations charities were being frozen out of contracts in favour of private companies.

Department for Work and Pensions statistics published yesterday showed 800,000 people took part with only 31,000 remaining in a job for more than six months.

Employment Minister Mark Hoban highlighted the fact 56% of people who joined the scheme have come off benefits.

He also insisted the Coalition had transferred the risk on to the private sector and that companies would not get paid if they did not deliver.

He added: "No-one should underestimate the challenges some of the providers face in getting some of the hardest-to-reach back into work."

Labour leader Ed Miliband called the scheme a "miserable failure" while Shadow Scottish Secretary Margaret Curran said: "It is a tragedy for every person who is trying to find work."

TUC general secretary Brendan Barber said it "beggared belief" ministers were trying to spin the figures as good news.

The Employment Related Services Association, the trade body for the welfare to work industry, said the criticism was unfair and predicted success rates would improve. It added the programme was proving better value to the taxpayer than any comparable welfare to work scheme in the past 20 years.

Dave Simmonds, chief executive of the Centre for Economic and Social Inclusion, said: "These are early days and more recent data suggests that Work Programme performance has picked up considerably in 2012. Our modelling suggests the Work Programme may now be running ahead of profile, catching up some of the lost ground and performing above the benchmarks set by DWP. We shouldn't rush to judgment."