THE headteacher at Queen Elizabeth High School in Carmarthen has described the Welsh Government's performance banding of schools as unfair, with some schools not being compared like for like.
Peter Spencer has also criticised the GCSE English exam grading "fiasco" as having an effect on the school's performance.
The school was among three in Carmarthenshire given the lowest band five rating — it dropped from two to five.
Banding is the Welsh Government's attempt to judge school performance on a broader basis than just exam results.
Mr Spencer said: "Aspects of the banding system are unfair as certain schools are not being compared like for like.
"QE High has a highly effective additional learning needs unit, Canolfan Elfed, which represents an outstanding model of inclusion.
"Approximately 70 of our pupils attend Canolfan Elfed and whilst these pupils make excellent progress, few achieve the mainstream education thresholds on which the bands are calculated.
"This factor alone places the school at least one band lower than a school without such provision."
However he said the banding did have a positive effect by using a range of data but said findings fluctuated year on year.
Mr Spencer added: "The current banding system will be confusing over time.
"The way calculations are made, year on year fluctuations are inevitable as has been the case nationally this year. Our overall results last year fell below our best ever in 2011, a key factor being the national GCSE English fiasco which had a significantly greater than average impact upon our school."
However he is confident the school can achieve better results in future and return to form.
Not one school in Carmarthenshire or Ceredigion was awarded a top banding.
The others to receive a five banding were Ysgol Y Gwendraeth in Drefach, which went from three to five, and Glan y Mor in Burry Port, also falling from three to five.
One school which remained the same, at band 2, was Ysgol Gyfun Bro Myrddin in Carmarthen.
But despite its relatively high grading, head teacher Dorian Williams said he was "frustrated" to have remained the same, despite being a "successful school".
"I am actually very pleased with our GCSE results this year, 75 percent achieving L2 inclusive of Welsh/English and Mathematics," he said.
"Last year's results were equally impressive and we therefore remain in band 2.
"I am, however, very frustrated that successful schools like Bro Myrddin are stuck in the same band because we do not fluctuate in our results from year to year.
"To achieve band one status we need to have poor results next year at GCSE level and return in the following year to our usual success rate.
"I do not wish this to happen."
The system has been a failure according to teaching union NUT Cymru and NASWT argues banding crudely ranks schools in a league table, failing to give any meaningful information on performances.
Carmarthenshire Council director of education and children's services Robert Sully said the banding results were mixed but that the authority was working with schools to improve the results.
Education Minister Leighton Andrews said the banding results gave a clear picture of how schools performed and was committed to the banding process.