The move comes amid concerns about lack of pupil progress and poor teaching in science. It follows the Government's move to extend the literacy and numeracy strategies from primary into secondary schools.
Officials are drafting the strategy, which aims to raise teaching standards through training and staff support. It is expected to be less comprehensive than the literacy and numeracy strategies and to focus on specific weaknesses identified by the Office for Standards in Education.
The strategy will be piloted in 200 schools from September and, if successful, be implemented by all secondaries from September 2001. The initial schools will be the same 200 that are piloting the literacy and numeracy strategies.
The move follows an OFSTED report, published last month, which found that pupils are not making enough progress in key stage 3 science. Inspectors said that secondary teachers were failing to buld on the success of primary science and were not challenging their younger pupils.
The report also said science teaching standards in the early secondary years lagged behind other subjects. Only a minority of pupils take part in high-quality experimental science - which is often ignored until they are 14.
In January, Education Secretary David Blunkett said that the progress pupils currently make in their first three secondary years should be achieved in two years.
Primary national test results in science have improved steadily in the last four years, with 78 per cent of pupils reaching the target standard last summer. But scores for 14-year-olds have remained constant at around 55 per cent.
From September, 200 schools in 17 local authorities will pilot new structured methods of teaching science, literacy, numeracy, science and thinking skills.
A spokesman for the Department for Education and Employment said: "As with literacy and numeracy we will provide training to support teachers."