Teaching unions fear that Estyn could be dragged into a political row after the education minister asked the Welsh inspectorate to investigate school reorganisation plans.
In the annual letter setting out Estyn's remit for the forthcoming financial year, Leighton Andrews said he wants inspectors to look at how education is delivered in schools of different sizes, and the issue of surplus places.
But there are concerns that the inspection body could compromise its neutrality by becoming involved.
Although the chief inspector's annual report highlighted the limited progress made by local authorities in school reorganisation and reduction of surplus places, it shied away from making specific recommendations.
In this year's report, then chief inspector Bill Maxwell said school organisation was the weakest service area inspected, and local authorities were "generally too slow in addressing the challenge of unfilled places".
In his letter to Estyn, Mr Andrews said: "Whilst there is increasing evidence that local authorities are tackling the results of falling rolls and seeking to organise more efficiently, progress by some has been limited.
"In order to widen our evidence base for the importance of strategic planning of school places, I am interested in exploring issues of efficiency in the delivery of education in schools of differing sizes and with different characteristics."
Dr Philip Dixon, director of the Association of Teachers and Lecturers Cymru, is concerned at the prospect of Estyn becoming involved. "If we are not careful, we risk politicising the inspectorate. Estyn must not become dragged into a political minefield like this because it could have very big ramifications on the ground," he said.
Dr Dixon believes that the Government must set out a clear methodology for the work it expects Estyn to do and to explain exactly what it means by "issues of efficiency". He said: "We are concerned that talk about efficiency doesn't simply become a cloak for cutting quality and axing jobs."
But Ann Keane, Estyn's interim chief inspector, said she welcomes the opportunity to become involved.
She said: "The Government is not asking us to take a direct view of specific local authority reorganisation plans, which would be interventionist, but to explore issues of efficiency in terms of different sizes of schools and to look at the whole issue of value for money.
"We have done that in the context of individual schools, so this allows us to take a step back and look more strategically."
TES Cymru understands that Estyn and government officials have already started to discuss the project and are expected to report back to the minister by August.
An Assembly Government spokeswoman said: "Estyn's annual reports have regularly drawn attention to the number of unfilled school places. The letter to the chief inspector indicates that a potential project dealing with school reorganisation, with a particular focus on efficiency, is to be discussed between officials of Estyn and the Assembly government in the near future."