In one of the strongest criticisms of the curriculum in recent years, the report says these subjects require a "fundamental and comprehensive" review.
The STEM report (School to University Transition in Science, Technology, Engineering and Mathematics) says the current science curriculum is "seriously out of step with modern requirements" - and recommends that "scientific literacy" be introduced to science courses for all pupils.
Science subjects are seen as overloaded and "lacking in obvious relevance to everyday life", while research needs to be done on how to engage pupil interest, the report comments. It wants more understanding of the core principles of the sciences and more extended practical work.
The quality of maths teaching is also called into question and the report urges an improvement in mastery of basic techniques, particularly algebra.
Maths skills should be reinforced in the science curriculum, the authors suggest.
Professor John Coggins, dean of the faculty of biomedical and life sciences at Glasgow University, who chaired the project, said: "Skills with numeracy and literacy are overwhelmingly important if you are going to do anything in industry or university. A large part of the report concentrates on our concern that the curriculum is based too much on assessment. We should trust teachers to do most of the assessment. We have good teachers in Scotland, and we have to give them a chance to get on with the job."
Professor Coggins was disappointed that pupils with excellent communications skills were being encouraged to take subjects such as media studies and not science. "We have a big problem with the failure of scientists to communicate well with the public."
There are other weaknesses. "What we are finding in universities is that a lot of the kids have disappointing problem-solving skills," Professor Coggins said. "The underlying reason for this is that they are very bad at algebra."
He added: "We want kids with enough confidence so they can recognise that there is a way of solving a problem by writing an abstract formula down and beginning to reason the problem out for themselves, rather than having broad themes of knowledge in physics, chemistry or biology.
"We want more on the basics which would then allow teachers to choose from a menu of specialised topics to illustrate problem-solving. If you strip out the sheer breadth of the syllabus, a science teacher could then introduce current topics like climate change or avian flu."
The report adds that an urgent review is needed of technological studies - the only school subject linked explicitly to the world of engineering. It also criticises schools for giving "a misleading impression" of computing science as it is studied in higher education.
The findings are currently being studied by the science review group set up following publication of the Scottish Executive's reform programme in A Curriculum for Excellence.
Stuart Farmer, president of the Association for Science Education in Scotland, said he supported "the broad tenor" of the report. The association wants to see an end to the current division of science into three main subjects. Mr Farmer believes this "separatist culture" leads to uninspired teaching, especially in S1 and S2.
An Executive spokesman said the science review would take full account of the STEM findings.
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