Inspectors, however, found clear evidence of widespread improvement in primary school courses sparked by the 2000 HMIE report, Improving Science Education 5-14. Over a recent one-year period, 70 per cent of primary schools inspected had good or very good programmes, compared with just 42 per cent between 1995 and 1998.
The Executive's "science strategy" cash was also beginning to make a difference.
The report comes as science teaching in primary and secondary schools is facing a major overhaul as one of the top priorities for reform recommended in the Scottish Executive's report on A Curriculum for Excellence.
While recognising the strengths in Scotland's science teaching, Graham Donaldson, senior chief inspector, says too many pupils leave school with little interest in science and insufficient awareness about its influence on their lives "More needs to be done to enthuse all young people about science and to make sure that courses are updated to reflect and excite interest in the latest developments and discoveries," Mr Donaldson states. "The knowledge and skills of our teachers also need frequent refreshing to ensure relevant and effective teaching and learning."
The key challenge to policy-makers, according to the HMIE report, is finding a way to respond to the explosive growth in science knowledge and skills. "The lack of any national mechanism to deliver high-quality professional updating to all science teachers is a major barrier," it states.
The report, Improving Achievement in Science in Primary and Secondary Schools, is based on an analysis of inspections between 2001 and 2004. It covers the primary and secondary stages up to Standard grade.
The evidence reveals a "very mixed and quite complex picture", HMIE states.
Pupil attainment is strong from P1 to P4 and in the separate sciences at S3 to S6, but "in need of significant improvement" at P5 to S2 and in Standard grade science, where results are "unacceptably low".
International comparisons reinforce the concerns, with science achievement in Scotland standing still since 1995. Pupil performance is significantly poorer than in many countries including England.
The disparities can only be exacerbated, experts fear, by the new science centres springing up around England which are attracting pound;25 million in funding from the Department for Education and Skills. A nominally UK centre is also being built in York with a further pound;25 million from the Wellcome Foundation.
These centres will deliver high-quality continuing professional development to teachers, technicians and assistants south of the border, so they can "lead the world in science education by 2015". Nothing comparable has yet been announced in Scotland.
Many of these, inspectors say, are now asked to transmit science content they have never learnt and skills they have never acquired. While some teachers make good use of such CPD as exists in Scotland, many are "unable to take advantage of these opportunities".
There is now an urgent need, the report states, for "a clear strategy" to ensure that all teachers of science are brought up to date.
HMIE calls for a mechanism for continually updating the curriculum to reflect new developments and an updating of courses to reflect contemporary issues. It also suggests there is a need for courses for non-specialists.
Inspectors pinpoint S1-S2 as the key stage where pupils are being turned off science. There is said to be insufficient collaboration with primary schools, very little differentiation, no discussion of social and ethical issues, and a "failure to capture pupils' interest and to challenge them".
In primary schools, the most common weaknesses are the lack of a clear place for science in the curriculum and poor continuity and progression.