Regulator Ofqual has made exam boards take immediate action after finding science GCSE standards had fallen.
Maths and English literature standards had been maintained but science was "clearly a cause for concern", it said.
Its evaluations involved not only the new general science GCSEs but also the separate physics GCSE. It is now going to check biology and chemistry.
The Conservatives called it a "terrible indictment" of the government. Ministers said they were "concerned".
As England's regulator Ofqual looked at exams set by the three main England-based awarding bodies - but their exams are taken also by many pupils in Wales and Northern Ireland and its findings have been copied to the equivalent bodies there.
It reported: "The results of our monitoring of the new GCSE science specifications in 2007 and 2008 and the review of standards in GCSE physics in 2007 raised significant causes for concern."
Ofqual's chair, Kathleen Tattersall, said: "Our monitoring shows that the revisions to the GCSE science criteria in 2005 have led to a fall in the quality of science assessments."
The boards' syllabuses were "over complicated" and gave students too many optional ways to obtain the qualifications.
This had made it difficult to compare their achievements. And there was too much emphasis on multiple choice questions, known as "objective tests."
Ms Tattersall said the QCA was again reviewing the GCSE science criteria with a view to new specifications (syllabuses) being in schools and colleges ready for first teaching in 2011.
"Science is a vitally important subject and it is essential that these new criteria and specifications should engage and challenge all learners, particularly the most able."
She added: "It is absolutely essential that standards remain consistent from year to year and across awarding bodies."
The mathematics and English literature reports had been reassuring, concluding that standards had generally been maintained. Minor issues were being addressed.
Ofqual said changes for 2009 include:
• Improved quality of questions, to stretch and challenge all students
• Work, including training for senior examiners, to improve objective tests (multiple choice)
• Tighter marking criteria to ensure that only the answers deserving of the marks are credited
• Some internal assessments revised to ensure better challenge to students
Schools Minister Jim Knight accepted there was a "serious problem" with the GCSE science exam.
He told BBC Radio 4's Today programme it was worth remembering, however, GCSEs tested a range of abilities from A* students to F-grade students, which was why some questions did not seem particularly challenging.
He also pointed out that although assessment was a problem, science learning was strong.
"Just because we have a problem with the way the knowledge is being assessed, it does not mean the knowledge is not there," he said.
Critics of the changes to GCSE science courses in 2005 warned even before they were implemented that they involved the "dumbing down" of the subject.
Exam boards defended their position. Greg Watson, chief executive of OCR, for example, said: "The report has little to do with standards or with content.
"It is mostly about whether the construction of the GCSE allows exam boards to assess scientific skills and knowledge in the best way - given that society wants 'science for citizens' and 'science for scientists' taught at the same time."
Shadow schools minister Nick Gibb said: "Ofqual confirms that the government has devalued science exams."
He added: "This is a terrible indictment of the government and the QCA at a time when scientific education has never been so economically vital".
Teachers' unions expressed concern that the reports might undermine confidence in the qualifications already gained by students.
The head of the Association of School and College Leaders, John Dunford, said: "I am extremely concerned that the report on science GCSE will damage the reputation of GCSE generally."
The Headmasters' and Headmistresses' Conference of leading independent schools said the "damning verdict" helped to explain why so many were turning to the International GCSE.