Business minister Michael Fallon told a House of Lords Committee last week that the Treasury and the Business department were working on a plan to "get to the bottom" of where the loans are going to.
"It's important we increase the transparency as to where lending is actually going," he added. "We're looking very hard with the Treasury at what information can be made available."
The £80bn FLS was launched in June 2012 as a replacement for the short-lived National Loan Guarantee Scheme (NLGS) in a bid to increase the volume of loans to homes and businesses. Participating banks can access funds at below market rates subject to them expanding their own lending levels.
However, figures for the first two months of the FLS published by the Bank of England showed that net lending decreased by more than £1bn across the six banks that drew funds from the scheme during the period. The next FLS figures, for Q4 2012, will be published in March.
Fallon said that there was not enough evidence that the FLS was helping credit-starved small companies, adding: "We need to make sure that taxpayer-funded schemes are getting through to the SMEs that need it."
Jamie Nelson of Compass Business Finance told PrintWeek that it was "absolutely sensible to drill down and get to the detail required on where the money is actually going".
"There is a big feeling in the market that it's not necessarily getting to the right people," he added. "The people that seem to be getting FLS money tend to be good credits that are then getting their interest rate subsidised by 1%.
"It's effectively subsidising investments of companies that would have invested anyway but it's not going to any of the credit-starved companies because those companies are still being turned down on their credit-worthiness."
Nelson said the Enterprise Finance Guarantee (EFG) scheme was "slightly different" in that the government was providing an element of added security by reducing the amount the funder had to lend against a particular asset, thereby lowering the risk.
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