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The £150m scheme, which encourages adults to update their skills, was put on indefinite hold last month following allegations of fraud by training providers.
But its suspension has thrown into question the future of IT training programmes worth up to £250 per person created to help unemployed people find work in deprived areas.
Plans by the TUC to offer courses in Microsoft applications and the European Computer Driving Licence to workers in the Liverpool area hang in the balance, following the suspension of the grants.
"I know education is the way out of the circumstances that people find themselves in but if someone in Salford has a spare £250 they are going to find a better use for it than training," said Stan Holland, who runs the scheme.
Other programmes at risk include the Everton Development Trust, which has trained 150 unemployed people in IT skills over the past two years, a community training programme in Henley, and The Internet Exchange, which runs 38 training centres across the UK.
About 8,500 people filed formal complaints about the scheme in October. A quarter were concerned with mis-selling or potential fraud, education secretary Estelle Morris disclosed in Parliament last week.
But trading standards officers believe that this is could be the tip of an iceberg, with many people unaware that training companies have cleared their learning accounts of money.
The Conservative party has written to the Public Accounts Committee calling for an investigation into the Government's management of the scheme.
Morris played down the scale of the fraud, saying only four training providers and 30 people were being investigated by the police.