Education officials say primary and secondary schools have not yet developed the robust assessments of science learning demanded as part of the new curriculum.
Under the Government's controversial reforms for what is taught in schools, the Curriculum for Excellence (CfE), schools are expected to monitor the progress of pupils from primary to the end of the third year of secondary, when study for formal exams begins.
However, an update on science teaching by inspectors from the Education Scotland schools quango raises serious concerns about current progress.
Last year, a House of Lords report stressed the importance of more pupils studying science qualifications to safeguard the future of the UK economy.
The Education Scotland report states: "Primary and secondary schools are not yet at the stage where they can provide sufficient evidence of learners' achievement in the sciences.
"Most schools do not yet have comprehensive approaches to assessing and tracking learners' progress. As a result, they do not yet have a robust picture of learners' achievement in the sciences."
In addition, Education Scotland said some secondary schools were still getting pupils to choose science subjects too early, which was impacting negatively on the breadth and depth of their learning.
And in primary schools it said learning in the sciences was "too often predominantly or exclusively" delivered through joint projects which did not feature enough science.
"A few children in primary school, whose experience of the sciences was exclusively through an interdisciplinary approach, could not identify having studied any science," it adds.
Eileen Prior, executive director of the Scottish Parent Teacher Council, described the report as concerning. "Parents are looking for a clear understanding of what their children are learning and what they are achieving and the report indicates there is some way to go before parents can be confident," she said. "We are particularly concerned early choice of subjects continues to be an issue."
Larry Flanagan, general secretary of the Educational Institute of Scotland teaching union, said the pressure to introduce new qualifications had forced many schools to take a pragmatic approach. He said: "Our call for a delay was dismissed by the Scottish Government. While teachers are determined to ensure pupils are not disadvantaged, the system needs to recognise that this is an interim phase."
Mr Flanagan also said it was important schools avoided excessive monitoring of pupils which would add a significant workload without improving learning.
The report also found that in some secondary schools there were still clear gender differences with girls tending to study biology and boys taking physics.