Inspectors who carried out the inquiry into reading in the London boroughs of Tower Hamlets, Islington and Southwark had had the final draft of their work changed.
The charge was denied by the chief inspector, Chris Woodhead, who said the data in both versions was consistent.
"If it is political to write as clearly as we can about the fact that significant numbers of children from our most disadvantaged communities are not learning to read then I would like somebody to explain what the word 'political' means," he said.
Reading scores collected during the inspection showed that eight out of 10 pupils were below average, but in government tests only three out of 10 had failed to reach expected levels. The inspectors' results were in the report but the discrepancy was not highlighted.
The boroughs, which were sent a copy of the report, said that a sentence which said reading was "well organised in three out of five classes" was altered to say that "weaknesses... affected the teaching of reading in two out of five classes."
Where reading had been classed as "satisfactory or better in approximately two thirds of the lessons" it was now "unsatisfactory or poor" in one third.
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