There are now multiple versions of science at GCSE level
Two of the big exam boards were still "generous" in the A and C grades they awarded in GCSE science exams this year, English regulator Ofqual says.
Ofqual made checks after identifying concerns, including a "lack of challenge", in some questions in 2008.
In a new report it said changes had been made - but many candidates already had some of their marks from units they took before those changes.
It said OCR and Edexcel were more lenient than the other big board, AQA.
Ofqual said: "We asked awarding bodies to address the findings of our March report in their grade awarding in summer 2009.
"Our monitoring shows that, as far as was possible, this was done.
"However, we were aware that many of the students who were 'cashing in' their units for GCSE results in summer 2009 had unit results already banked before the actions taken in summer 2009."
The watchdog said it recognised that change would take time to work through.
One of the issues it had identified was the variation in types of assessments used and the weightings allocated to these.
"This cannot be addressed until the specifications are replaced with revised versions, written to meet different subject criteria."
The Qualifications and Curriculum Development Agency has been asked to take this into account as it draws up yet another new set of criteria for science.
An OCR spokesman said: "The issues with science are historic problems with the new style of specifications. We are working with the regulator to ensure that standards are aligned across the awarding bodies.
"We are currently half-way through a two-year programme and expect that by summer 2010 these differences will have been substantially reduced."
Edexcel declined to comment.
The chair of Ofqual, Kathleen Tattersall, said it had been a successful exam season.
"I was fortunate enough to experience first-hand the reactions of students who were receiving their results and was able to congratulate them on their achievements," she said.
"Several new and revised qualifications were awarded for the first time. These included revised AS-level qualifications and the principal learning and project qualifications in the Diploma.
"I can assure learners, their families, employers and providers of further and higher education that examinations were well delivered this year and that standards are being maintained."
In recent years science at GCSE level has been changed from a double award to a core subject plus additional science, which is taken by most science pupils. There are also separate chemistry, physics and biology qualifications.
The government has given all pupils who are working at the expected level when they are 14 an entitlement to study the separate sciences if they wish - but has not made it a requirement for schools to teach them.