Gillian Shephard, the Secretary of State for Education, ordered the inquiry after her advisers on exams discovered discrepancies between exam boards in the two subjects at the boundary between grades B and C.
They found bigger increases in the proportion of B grades awarded by two boards, the Southern Examining Group and the University of London Examination and Assessment Council, than by the other three boards. About one-third of the total entries in maths and science received B and C grades. No candidate will be downgraded. Several thousand candidates' papers, mostly in maths, are thought to be involved.
Mrs Shephard said: 'It is essential that GCSE grades are consistent and fair across the country.' She said the record overall proportion of candidates gaining grades A-C was not affected. The School Curriculum and Assessment Authority will conduct an urgent review to be completed next month.
Exam board officials said the most likely explanation of the discrepancies was a change in the rules for awarding grades. In maths, pupils sit different papers according to ability. Last year the top grade for those sitting the intermediate papers was a C. This year they could be awarded a B.