As primary schools began operating the new literacy hour - part of the #163;59 million strategy - new research revealed a crisis of confidence among secondary heads.
Initial findings of a three-year study by academics at Reading University disclose widespread uncertainty among secondary heads about how to orchestrate literacy improvement and even what literacy is.
The study poses a considerable challenge to the Government's crusade on standards and raises questions about its focus on primary schools. It is hoped that success in primary schools will have a knock-on effect in secondaries where many staff already feel ill-equipped to cope.
The research, conducted by Winston Brookes and Andy Goodwyn from the School of Education at Reading, reveals that most secondaries do not have a whole-school policy on literacy.
Headteachers in more than a third of the schools interviewed admitted that even their English departments did not have a policy. Two-thirds did not consider their schools examples of good practice.
The study, based on a survey of 120 schools in the Home Counties, reveals deep confusion among secondary heads about what literacy is and real worries about funding and training.
And Mr Brookes said: "Clearly there is a need for a co-ordinated strategy, resources, training and for teachers to have some understanding of what people are talking about in terms of literacy.
"It is right to concentrate on primary as the Government has, but it is going to cause problems for secondary schools and they don't know what to do.
"They don't feel skilled enough and don't feel well-resourced enough."
The Government drive to improve literacy has so far concentrated on primary schools in an attempt to meet its target of 80 per cent of 11-year-olds reaching level 4 or above in English by 2002.
The Reading research, however, revealed that secondary heads question whether level 4 is a trustworthy indicator of literacy. They are also troubled by weaknesses in the primary-secondary transfer system.
Despite their deep concerns, most of the headteachers said that literacy was an important focus and that they believed they could raise standards. They just needed support and training.
Mr Brookes added: "If children do make good progress it is going to have implications for secondary schools. It is not going to undo the good work though."