Hywel Jones, a statistician at the Welsh Language Board (WLB), compared results for the two subjects from key stage 1 to GCSE. He found pupils at Welsh-language schools did just as well or better at both GCSE and KS3.
In 2005, 58 per cent of GCSE science candidates assessed in Welsh gained an A*-C grade at GCSE, compared with 56 per cent taking the English exam. In maths, 57 per cent of Welsh-speaking entrants gained A*-C, compared with 54 per cent.
Similar results were also found in KS3 assessments, with more Welsh-language pupils achieving level 5 or above. The WLB hopes to end the myth that sitting Welsh-language exams in these subjects puts pupils at a disadvantage, leading to some schools swapping to English.
Higher-performing Welsh-medium schools are often seen as a reflection of their middle-class intake of pupils. But Mr Jones compared schools with similar numbers of pupils eligible for free school meals.
He said it was amazing that some schools in traditional Welsh-speaking heartlands dropped Welsh in maths and science.
Gruff Hughes, general secretary of the Welsh-medium teachers' union UCAC, said young people studying science in Welsh also learn English terminology, which equips them for further and higher education courses, where they might not have access to a Welsh-speaking tutor.
"The skills pupils learn in science and maths are the same whatever language they are in," he said.
A study by Oxford university in 2005 found that students who are taught maths in Welsh learn better number recognition than in English.