The proposal - a key recommendation of the Furlong review on teacher-training - could also make it harder to attract a wider range of people into the profession, such as career-changers and people from ethnic minorities, according to the Universities Council for the Education of Teachers (UCET) Cymru.
Teacher-training overall currently accounts for more than half of the Welsh-medium provision in higher education. UCET Cymru says its members have also had more success attracting "non-traditional" students into undergraduate teacher-training.
Furlong favours the development of "pre-professional" education degrees leading to one-year postgraduate certificate in education courses - or training for related jobs, such as counselling and early-years support.
A UCET Cymru spokesperson said undergraduate primary courses attracted applicants, and are welcomed by schools and local education authorities.
He added: "Replacement with a three-year pre-professional course plus a PGCE presents uncertainty. We are not convinced the risk of undermining progress against the advantages of widening participation and Welsh language has been fully assessed."
Assembly members met yesterday to discuss responses to the Furlong review, which also proposes cutting primary teacher-training numbers by half and secondary trainees by a quarter.
Both UCET Cymru and Higher Education Wales (HEW), which represents the country's vice-chancellors and principals, have warned against big cuts in secondary numbers.