Figures from the Welsh Assembly show that in some areas almost half the pupils who speak Welsh as a first language are taking the easier exam.
There are two forms of Welsh-language exam. One is intended for fluent speakers who use Welsh at home or have attended a Welsh-medium school. The other is for pupils who have learnt the language in the classroom.
Across the principality 19 per cent of pupils are taught Welsh as a first language at key stage 1. This drops to 13 per cent by Year 11.
The trend is particularly pronounced in a few, primarily Welsh-speaking, authorities. In Carmarthenshire, 51.4 per cent of pupils are assessed as first-language speakers at KS 1. But by KS3 only 27.9 per cent are assessed in Welsh.
In Ceredigion, 74.3 per cent are regarded as first-language speakers at KS1, but only 55 per cent claim similar status at KS3.
In Gwynedd, 94.7 per cent are first-language speakers at KS1, but only 78.8 per cent say they are at KS3.
The Assembly has commissioned Accac, the Welsh qualifications and curriculum authority, to conduct an investigation.
Many headteachers believe that the number taking the easier exam is a direct response to the pressures placed on schools and pupils.
Neil Foden, head of Ysgol Friars, Gwynedd, said: "There are a lot of children who expect a row of A* grades at GCSE, and a C or a D in first-language Welsh.
"They see that as a failure, and that's something they're not willing to countenance.
"Having pupils with D grades is going to affect schools' exam statistics.
We are under pressure to achieve quick, short-term success."
John Williams, Accac chief executive, said there may be other reasons for pupils not claiming Welsh as their first langage.
"Many of these areas are rural with very small schools," he said.
"Gathering pupils together is enough of a challenge, without distinguishing between first and second-language speakers.
"We need to drill down below the raw statistics to find out what the real issues are."