Some specialist Welsh teachers could see their pay sliced by almost Pounds 1,700 per year, according to Welsh-medium teaching union UCAC.
The union says some local authorities plan to snatch back management allowances from athrawon bro (area teachers) and not replace them with more expensive teaching and learning responsibility points. If the lowest TLR payment were awarded to the peripatetic language-support teachers, it would mean an extra pound;612 in their pay packet.
Meanwhile, Welsh teaching unions are gearing up to fight schools on behalf of members who have lost out under the new arrangements. Two indicative ballots have already been held in Wales and a third is on the cards.
And new research suggests heads of maths, English and science departments in secondary schools are getting a better deal under TLRs than colleagues responsible for non-core subjects.
Management allowances ended on December 31 and have been replaced by TLRs - intended to reward teachers with significant responsibilities for teaching and learning. Schools can phase them in over three years, with existing salaries safeguarded until 2008.
Welsh schools have until March 31 to produce new staff structures setting out TLR positions. Local education authorities employ Wales's 200-odd athrawon bro and will make their own arrangements. UCAC has written to Jane Davidson, the minister for education, lifelong learning and skills, asking her to intervene on behalf of the Welsh specialists.
She has replied saying LEAs must have regard to statutory guidance when considering athrawon bro for TLRs. But the Assembly government cannot get involved in "technical matters" because pay and conditions have not been devolved from London.
The union's Elaine Edwards said: "We have serious concerns about a few counties where already the teachers in the athrawon bro service are not classed as teachers at all, and so are not governed by the national teachers' pay and conditions document.
"Paying specialist teachers less for the same work will only lead to more retention and recruitment problems. Without experienced, specialist teachers to motivate pupils, how can we ensure Wales will become a bilingual nation?"
Janet Ryder, Plaid Cymru's shadow education spokeswoman, has also called for a review of how the pay changes work in Wales. The National Union of Teachers Cymru has already carried out indicative ballots at two schools - one primary, one secondary - where staff are in dispute with management over TLRs.
David Evans, Wales officer, said: "We would like to negotiate with schools to avoid formal ballots. But if there is no change we would take the appropriate action.
"The aim is to ensure our members don't suffer, and that schools themselves don't suffer by having disenchanted staff."
Teachers' union the NASUWT Cymru is also considering a strike ballot at a school in Torfaen.
Schools are making up their own pay-scales for senior jobs, leaving teachers baffled by what to expect. They should only be advertising managerial posts at either TLR2, worth between pound;2,250 to pound;5,500 extra, or the greater TLR1 (pound;6,500 to pound;11,000).
But in job adverts, schools have been inventing their own scales - such as "TLR1.4", "TLR1D". A few believe, mistakenly, that TLR2 is bigger than TLR1.
Research carried out by Oxford-based research company Education Data Surveys also shows that heads of science, English and maths took the lion's share of TLR1s advertised last month.
Heads of music, art and design, history, geography, drama and citizenship were normally offered the lower pay bonus.