The Mentoring and Befriending Foundation persuaded other organisations to collaborate in a bid to provide mentoring to people seeking employment.
It planned to submit an application to the BLF's Research Programme in time to meet this month's deadline for the second round of funding.
But the BLF has now abolished the second round and charities have been told they must wait to apply in round three, on which decisions will not be made until October 2009.
The BLF has also reduced the total value of the programme from £25m to £20m (20 August, page 3).
Steve Leach, deputy chief executive of the foundation, said keeping together the partners that collaborated on the bid for another year could prove impossible.
"We have worked hard to get a national provider interested, as well as a major research university and direct deliverers, and we feel this arbitrary decision may well sink the initiative," he said.
Momenta, the company delivering the programme on behalf of BLF, wrote to applicants saying the timetable had been revised because of the high volume of interest.
It said it had received just over 250 applications for round one, of which 88 were potentially fundable. "If we maintain three rounds of funding, we will be able to fund only 12 of these applications with the money we have," it said in its letter.
Leach said it was "disingenuous" to blame high demand for delays in decisions, and accused the fund of a dismissive attitude.
A BLF spokesman said reducing the number of rounds would be a better use of its resources and those of its applicants.