In a response suggesting she would not bow to pressure from education unions, Susan Lewis staunchly defended use of the information, claiming it was popular with teachers, parents, governors and local authorities.
Schools that did best in Estyn inspections during 2005-6 are colour-coded green in the report. However, Ms Lewis denied the information was a crude league table, saying inspection grades already took into account the full circumstances that schools and teachers worked under.
She also said the information was already easily accessible online and her report simply pulled it all together. "It is important to provide information about public services so people can make informed choices," she said.
Education unions joined forces last week to demand that the results are dropped from next year's report. But sources close to the Welsh inspectorate are questioning why the NUT Cymru waited till six months after the report was published to complain.
Jane Davidson, former minister for education, lifelong learning and skills, also sanctioned their use when approving the report despite being anti-league table, according to the source.
NUT Cymru secretary David Evans said in his letter to Ms Lewis: "The tables mean very little since only schools inspected that year are included.
Nevertheless they have caused considerable distress for members."
League tables were scrapped in Wales in 2001.