Under the regulations, which came into force on 25 April 2013, CIL charging authorities are required to transfer to town and parish councils up to a quarter of the levy receipts arising from development that takes place in their area.
But a Freedom of Information (FOI)investigation by Planning found that, despite collecting more than £9 million between April 2013 and June 2014, authorities had passed on just one per cent - £92,000.
Twenty-six of the 43 charging authorities had received payments, totalling more than £9.2 million, over the 15-month period, Planning's FOI requests found. But only eight - Broadland, East Cambridgeshire, Huntingdonshire, Newark and Sherwood, Shropshire, Waveney, Winchester and Wycombe - reported that they had passed CIL funds to town and parish councils.
The investigation uncovered payments to 56 town and parish councils in those areas, with the average sum transferred £1,648.
Ken Browse, chair of umbrella body the National Association of Local Councils, said the figures were "extremely disappointing".
He said: "They confirm our worst fears that the system is in danger of not being fit for purpose and needs an urgent rethink."
But a Department for Communities and Local Government spokesman said it expected the sums transferred under the mechanism to "start from a low base and steadily rise over time".
The spokesman said: "Receipts are passed on six months in arrears. The new provisions do not relate to planning permissions granted before the new rules." He added that the regulations make clear that councils must pass a proportion of levy receipts to their local communities.
Adrian Kerrison, who leads the Nationwide CIL Service, said the proportion of funding transferred could not be fully explained by the payments being made in arrears.
He said: "I can only conclude that most councils haven't yet set up the distribution procedure and are probably in breach of the regulations.
"Parishes in CIL charging authorities will need to take a proactive role in ensuring they receive the funds they are due."