The diploma, a qualification that at least one major exam board regards as "dead", has cost the taxpayer nearly #163;20,000 for every pupil completing it, The TES can reveal.
The figure, which does not include teaching costs, is almost twice the amount previously estimated. And the final bill, already hundreds of millions, could be higher still.
Professor Alan Smithers from Buckingham University said: "It is a terrible waste. The diploma doesn't have much recognition or open many doors."
The diploma was originally envisaged as a serious rival to A-levels and GCSEs. Ed Balls, former Labour education secretary, thought it could be the "qualification of choice" by 2013 and "the jewel in the crown of our education system".
But results released yesterday show just 9,069 of the diplomas aimed at GCSE-level pupils were completed this year, compared to 5.15 million GCSEs.
They are likely to drop further as this year's courses were begun before the change in government and the launch of its English Baccalaureate - both likely to further damage the diploma.
So far, only 15,063 students have finished a diploma at any level since it was first launched in 2008.
In the meantime, at least #163;295.6 million of Government money has been spent on developing the diploma, funding consortia and training staff to deliver it, and subsidising transport so pupils could reach lessons.
The figure works out at #163;19,624 per candidate, nearly four times the annual #163;5,083 average per-pupil school funding in England, and only covers diploma spending until the end of March 2010.
The diploma now appears doomed. The TES has learnt that ministers want to end the Diploma Aggregation Service (DAS) the Government currently provides to work out results for the hugely complicated qualification.
Ministers believe the diploma should not receive Government support that is unavailable to other qualifications.
But they think exam boards should be able to continue to offer the diploma if they think there is a market for it.
Boards will not publicly reveal their hand until Ofqual has finished its consultation on the DAS. But they are highly unlikely to allow candidates to continue to take diplomas made up of courses from different boards, if they offer it at all.
One senior source from a major board told The TES that entry levels were "dire across the board". The "reality" was it might offer individual courses in two or three subjects at specific levels, but the diploma itself was "dead".
AQA said it was awaiting the outcome of the DAS consultation and OCR said it was looking at ways in which it could continue to provide the diploma.
An Edexcel spokesperson said: "We will be continuing to offer the diploma as long as there is sufficient demand from schools and colleges."