Acca's move, scheduled for the end of the year, follows long-standing concerns about the running of the scheme, which it set up in 1979 with the Institute of Chartered Accountants in England and Wales and the Institute of Chartered Accountants of Scotland.
It comes just days before the English institute is due to unveil fresh proposals for regulating its members and amid acrimonious disputes about financial services regulation.
The JDS was hit in late 1993 by the Court of Appeal's finding in favour of Price Waterhouse, which claimed it should not face a JDS inquiry while still fighting court action.
However, it is believed that the failure of a similar case brought against the JDS by Coopers & Lybrand over its role in the Maxwell collapse has strengthened the body. And some observers suggest the Acca announcement could be a ploy to reach a compromise on funding. Some members of the English and Scottish institutes have expressed concerns about costs, which has lead to an attempt to streamline the JDS.
Acca deputy president Peter Langard said: "JDS investigations are complex and as a result take too long and are not demonstrably effective."
The organisation, which says it has not referred a complaint to the scheme for more than 10 years, says it has to pay too high a proportion of the costs of the investigations. It anticipates that this year it will have to pay about pounds 750,000, or about 27 per cent of total JDS expenditure.
William Morrison, chairman of the JDS executive committee, could not be reached for comment.