The trailblazing Welsh Baccalaureate qualification for 14 to 16-year-olds is being badly undermined because results do not count towards headline performance figures, potentially damaging its reputation with parents and employers.
Estyn said this could be a "major stumbling block" to key stage 4 roll-out, despite being well received by teachers and pupils during the pilot, according to a report, The Welsh Baccalaureate In Key Stage 4, published last week.
The Welsh inspectorate also voiced schools' concerns that they may be unable to sustain the bac when extra funding of about pound;165 per pupil per year ends in 2009.
Some 2,300 pupils at 21 schools are piloting the qualification between 2006-9 at both foundation and intermediate levels. Inspectors are generally positive, praising good teaching, effective planning, strong support for pupils and high standards of work.
But they said this is being spoiled by the failure to include results in key performance figures.
"These indicators are the ones that attract most attention from parents and the media," said the report. "The fact that the qualification does not count towards them is a major stumbling block to its further expansion at KS4."
The full qualification has a "core" certificate - made up of key skills, modules on Wales, Europe and the world, work-related education, and personal and social education, plus an optional choice of four GCSEs or an equivalent.
Core certificate results will contribute to a wider points score, but not to high-profile data such as the new threshold indicators or the widely recognised five or more GCSE grades A*-C.
The Assembly government said this was because the core was "not a qualification in its own right".
Brian Lightman, president of the Association of School and College leaders (ASCL), and head of St Cyres School in Penarth, Vale of Glamorgan, said: "I've discussed this with the Assembly government and emphasised the urgency required to sort it out.
"It would be awful if the success of this qualification was held back because of what's essentially a technical point."
Mr Lightman, who has 62 pupils taking part in the pilot, added: "It needs to be publicly recognised in a way that employers can understand."
At another pilot school, Barry Comprehensive, head David Swallow said it was difficult to sell the bac to parents without "some sort of equivalence".
He stressed he was very positive about the qualification, but added: "It needs a high staffing content to deliver all elements, particularly the key skills. Without that extra funding, it makes it much harder."
The Assembly government said it would consider calls for extra financial support.
Responding to the exclusion of the bac from key performance figures, it said: "The core certificate is not a qualification in its own right and therefore does not have a separate threshold contribution. This is because the breadth that we want students to achieve is met by a combination of the core, which guarantees skills development, and the optional qualifications."
Chris Howard, vice-president of the National Association of Head Teachers and head of Lewis School in Pengam, said the government had been "overly conservative" in its attitude towards the place of new qualifications within the scoring regime.
He said: "If the Welsh bac counts for nothing in the measurement of school effectiveness at 14 to 16, it will hold back the development of a vital qualification."