Secondary schools are reporting a widening gap in the ability of Year 7s in modern foreign language classes.
The growing gulf is a consequence of languages being taught at key stage 2 in 118 of Wales's primary schools under a pilot scheme, and wide variations in language teaching, including Welsh, from an early age.
Uncertainty over funding is also causing some primaries to doubt whether they will be able to continue teaching an MFL, usually French, German or Spanish, to the same standard after 2009.
Meanwhile, the Assembly government says it has no plans to make MFLs compulsory for all primaries, despite new research which strongly backs the practice.
Some secondary schools have already devised schemes to help plug the divide between pupils taught more language skills at primaries. At one, pupils are able to capitalise on their skills in Y7 while helping classmates who may be struggling.
According to Antonella Sorace, professor of developmental linguistics at the University of Edinburgh, the earlier children learn a second or third language, the better.
"It has been shown that bilinguals tend to be better than monolinguals at multi-tasking. Some studies show that bilingual children on average learn to read earlier than monolinguals," she said.
Reversing a downward trend in the uptake of MFLs in Wales is the key aim of the Assembly-funded KS2 pilot project, led by Wales's National Centre for Languages (CiLT Cymru) and launched in 2003. The government claims it is too early to see if the pilot scheme has led to a language revival. But those undertaking the scheme see many benefits.
But teaching unions claim not enough is being done to encourage young people to take languages. A report from the Qualifications and Curriculum Authority this week also acknowledges that modern language GCSEs are graded more harshly than others.
Jacqui Roome is acting headteacher of Tir-y-berth Primary School in Caerphilly, where for the past two years a pilot scheme teaching Spanish has been extended to pupils in Y3-4. She says it has given pupils confidence.
"Even though they're going to be doing French at secondary school, learning those skills and nurturing the desire to learn languages is so important," she said.
This need for continuity is seen as especially important in transition from KS2 to KS3, the key aim of the second phase of the pilot project in Wales.
Research by the National Foundation for Educational Research found that a lack of communication between primaries and secondary schools in England could undermine young children's language learning, because information is not passed on to secondary teachers.
But schools are using transition schemes to good effect in Wales, including "language passports", where pupils summarise what they have learnt in KS2 and it is then passed to their Y7 language teacher.
Primary pupils in the catchment area of Ysgol Bryn Elian in Colwyn Bay are routinely invited to take part in the school's French and German language days, whether or not they are learning an MFL at school.
"The teachers are aware of differences in ability. We sometimes use pairs of pupils to teach each other, so they both benefit," says Michelle Jones, head of MFL at Bryn Elian.
But despite enthusiasm, Assembly funding for the pound;250,000-a-year pilot will end in July 2009, after which schools will be able to apply for a grant from the Better Schools Fund.
The future of MFL provision will also not be decided until the results of the pilot - due to end in 2009 - are published.
The Assembly government was criticised last year for not following England's lead in making MFLs compulsory for all primary schools in 2011.
An Assembly government spokesperson said officials would consider doing this only after the next national curriculum review.