Schools lack confidence in delivering the skills framework and devote too little space on the curriculum to teaching skills, according to early findings from a report by Estyn.
The Welsh inspectorate is working on a remit report into the impact of the framework, which was introduced by the Assembly government in 2008 to complement the revised national curriculum.
The non-statutory framework aimed to provide guidance for teachers on how to deliver thinking, communication, ICT and number skills for learners aged from three to 19 and beyond.
It was developed to help pupils whose needs were not being fully developed by a subject-led approach, and partly in reaction to concerns from employers about skills shortages in the workplace.
It said the skills needed to be "firmly embedded into the experience of learners across all their learning" to enable pupils of all ages to become successful in school, at home and in the workplace.
But chief inspector for Wales Ann Keane told TES Cymru that the early findings of Estyn's study were not positive.
"They are not giving me confidence that schools are confident about delivering the skills framework," she said.
"We have seen some very good examples of it in action, but in a lot of schools it tends to be fairly marginal to the timetable."
She said that while many primaries were delivering a theme-based curriculum, most secondaries have not radically altered their teaching.
Although some secondary schools launched successful schemes in Years 7 and 8, too many reverted to a subject-based approach in Year 9 in preparation for GCSEs.
The report said the curriculum revisions did not go far enough in allowing a more flexible, tailored provision in key stage 3. The remit report, due to be published in the next few months, will go into more detail and contain recommendations for the government.
But Ms Keane said: "We need to think about how we can better embed teaching of skills to pupils at all levels of the curriculum.
"There's scope to look across the subjects and say teachers shouldn't be just subject leaders, but where can they build on those skills in different parts of the curriculum?"
But, she added: "I don't think it's necessary to revise the whole curriculum. We need more flexibility to drive innovation and embed skills."
Robin Hughes, national manager of awarding body OCR Cymru, called for a debate about skills in the curriculum.
He said: "Do we want to teach skills at KS4 - what do we think these pupils need to learn?
"In science at KS4, we have been working to a more skills-based framework and we have seen increased take-up."
The Assembly government has said it will consider the chief inspector's annual report in more detail before responding.
- Original headline: Chief inspector voices concerns over failure to deliver on skills