Governors have demanded clear guidance from the Assembly government on a new policy that sets strict limits on how often teachers can cover for absent colleagues.
The "rarely cover" rule is set to be introduced in schools across England and Wales in September as part of the 2003 workload deal.
But there is widespread uncertainty among heads and teachers' unions about the practical and financial implications of the new rule. They fear it could prove costly and disruptive.
Now, Governors Wales, the organisation that represents school governing bodies, has written to Jane Hutt, the education minister, expressing serious concern and asking how she expects the "rarely cover" rule to be implemented.
Governors passed an emergency motion at the organisation's annual conference in Llandrindod Wells earlier this month. The motion also urged the government to pump more cash into schools, so heads can employ extra staff if they are struggling to provide cover.
Irene Cameron, a governor at St Julian's Comprehensive in Newport and chairwoman of the Newport association of governors, who proposed the motion, said: "We need to have clarification on this. There are going to be big financial implications here because extra cover staff are going to cost money. Will schools get extra funding?
"This will put heads in all schools in a very difficult position. Each head is going to act differently. There are governors who are not even aware of it."
Jane Morris, director of Governors Wales, said there was concern that the new rule could stop teachers taking time off for activities such as professional development courses and school trips.
Carol Sayce, the organisation's chair, said: "Governing bodies have very mixed views on what `rarely cover' actually means; there are different interpretations. We want clear information and guidance from government so we know exactly what this means."
In April, Welsh-medium teachers' union UCAC passed a motion at its annual conference calling for the government to give schools more cash to implement the "rarely cover" rule.
Members warned that the regulation could "cripple" schools and lead to widespread teacher redundancies if it was not properly funded.
Gareth Jones, secretary of heads' union ASCL Cymru, said heads are "extremely concerned" over the cost of the rule, which he said could be up to pound;20,000 per school.
In March, Ms Hutt promised an inquiry into how often heads and teachers cover lessons for absent colleagues, but the results may not be available before the end of the year.
A government spokeswoman said the Workforce Agreement Monitoring Group would be issuing guidance to help schools implement the rule from September 1.
The theme of this year's Governors Wales conference was safeguarding children in education.
Ms Hutt told delegates that governing bodies have a "vital role" to play in safeguarding pupils, and that they are "well-placed" to spot pupils who are at risk.
Margaret Davies, head of the ethnic minority and child protection branch of the Department for Children, Education, Lifelong Learning and Skills, said governing bodies should make sure their schools have effective child protection policies that are reviewed annually and made available to parents. She suggested that a specified governor should deal with child protection issues.
Tom Davies, the Welsh member on the Independent Safeguarding Authority board, warned governors that they would have to register with the ISA's new vetting and barring scheme for professionals who work with children.
From October, the scheme will be rolled out over five years as part of the Westminster Government's response to the Bichard Inquiry into the Soham murders.