Paul Black, emeritus professor of science education at King's college London, said that the short tests did not allow pupils to demonstrate a real understanding of the subject.
He said that the levels awarded were often determined by how pupils felt on the day and which questions were included.
Professor Black used his keynote address to call for radical changes to the way science is taught and assessed. He also suggested that there should be less emphasis on testing pupils' factual knowledge.
He said the testing regime, combined with pressure to boost schools' league table position, has ultimately led to "teachers teaching in a way they are not proud of".
"There is nothing wrong with teaching to the tests as long as the tests are good ones," he said. "The problem is teachers do not believe these tests are valid."
He estimates that about 30 per cent of pupils each year are awarded the wrong level in key stage 3 tests. In contrast, fewer GCSE students are given the wrong grade because the examination takes longer than the tests, he said.
Professor Black said GCSE grading could be improved by reducing the reliance on short questions which test recall of content rather than deeper understanding.
Pupils should be assessed by looking at a portfolio of their work, which could include longer projects more capable of demonstrating their ability to understand complex arguments about scientific issues, he said.
His comments come as exam boards work on new GCSE syllabuses with greater focus on investigation and ethical issues which will, they hope, persuade more pupils to continue with science post-16.
Exam boards will publish details of the changes in March but some fear that while they will follow the letter of the QCA's instructions, they will fail to embrace the spirit of reform.
Professor Black said teachers should hold fewer question and answer sessions and be more willing to involve pupils in discussions about ethical scientific issues so that they learn about the real world.
But pressure to achieve test results means that teachers will only change their pedagogy if there is a parallel change in the way pupils are assessed.
Exam methods do not allow pupils to demonstrate their understanding of ethical issues or to show a talent for scientific investigation, he said.