Peter Maddocks, head of Ysgol y Gader, Dolgellau, in Gwynedd, said the lack of interest could lead to a real shortage of Welsh-speaking heads in the region.
The NPQH became mandatory for all first-time heads in 2005. But education unions have already raised concerns that too few Welsh-speaking candidates are applying to take it.
"There is the real possibility of a crisis in recruitment of heads in this area," said Mr Maddocks. "If you are from the south, you'd probably want to stay there, not move to an isolated school in Gwynedd. Past experience shows that."
Mr Maddocks said there were too few applications for heads' jobs at present. Areas such as Dolgellau, in the heart of Snowdonia, are sparsely populated and Ysgol y Gader is one of the smallest secondary schools in Wales with just 323 pupils. It has no sixth form.
The Assembly government has said enough candidates are taking the NPQH, but Mr Maddocks said they were "mostly from the south".
Fears that an ageing population of heads in Wales could trigger a leadership shortage in the coming years have been long held. The National Association of Head Teachers Cymru has blamed the lack of aspiring heads across Wales on poor pay rises upon promotion.
Statistics from the General Teaching Council for Wales show that in 2006, some 60 per cent of heads in Wales were over 50 - 1,084 out of 1,797.
On the present intake, the Assembly government predicts there will be up to 1,700 NPQH graduates in Wales by 2010.
In March last year, 256 serving heads and around 750 teachers held the NPQH, and there are 170 teachers taking it this year.
Since it became mandatory for new heads, some 300 candidates have applied for the course, mostly from the south.
Estyn, the Welsh inspectorate, has warned that some prospective heads are being lost because the NPQH criteria are too narrow.
Acting heads filled a quarter of vacant posts in Wales last year, prompting Estyn to call for an investigation by the Assembly government in January this year. In the same report, the inspectorate also backed up claims that not enough Welsh-speaking teachers are gaining the qualification.
UCAC, the Welsh-speaking education union, has also called on the Assembly government to review the geographic and linguistic background of candidates selected for the NPQH.