Teacher trainers are still failing to instruct many new primary teachers properly in both reading and the marking of pupils' work, said a report from the Office for Standards in Education.
Trainees are rarely taught how to plan a programme of phonics - crudely, the sounding out of letters, the Office for Standards said.
Phonics are at the heart of the Government's new literacy hour, which aims to raise reading standards. Earlier this year Tony Blair attended a conference to promote phonics after inspectors found that many teachers did not know how to use them.
Inspectors visited all colleges, universities and school-based schemes involved in teacher training to investigate how they were teaching reading and number.
A report of their findings said that the national literacy hour, which was introduced into all schools last September, and the national numeracy hour, which will start everywhere after the summer holiday, are improving new teachers' methods and their ability to organise a class.
Most new teachers have at least adequate knowledge of reading, and training courses are putting more emphasis on phonics.
But the inspectors said that "trainees are rarely shown how to plan a structured programme of phonics teaching over a period of time in order to develop pupils' knowledge and skills systematically".
Training in how to mark and report on pupils' work also remains poor. Numeracy training is better: teacher trainers are now showing new teachers how to teach "accurate, rapid mental calculation".
And they are preparing them better to teach different methods of adding, subtracting, multiplying and dividing.
Fewer than half the courses that were inspected were good overall - 24 - compared with 34 which did not match up to government standards in at least one area.
Ministers have introduced a national curriculum for teacher training as part of a package of measures to improve the quality of new entrants to the profession.
David Taylor, Ofsted's head of teacher education and training, said: "The standards now required of trainees in relation to literacy and numeracy are rigorous and demanding.
"A number of policy areas are coming together to make sure that primary trainees will, increasingly, enter schools with the required competence and confidence.
"However, a minority of trainees still exhibit an unacceptable degree of uncertainty in their own subject knowledge and understanding.
"And not all courses are yet equally rigorous in what they expect of their trainees when assessing them for Qualified Teacher Status."
The report from Ofsted emphasised that there have been marked improvements in the training of teachers in reading and numbers and that, overall, only a minority of new teachers are ill-equipped for the profession.