The Qualifications and Curriculum Authority made its position clear during a row between ministers and the Government's Statistics Commission, which said in February that although there had been improvements at key stage 2, the test results substantially overstated the rise.
Senior civil servants are to meet commission officials later this month to try to thrash out their differences over the commission's report, which questions the extent of one of Labour's biggest education success stories.
Scores for 11-year-olds jumped from 48 per cent reaching the expected level in English in 1995 to 75 per cent in 2000.
But the commission said this rise was largely down to teachers drilling pupils for the tests.
However, the Government is fiercely contesting this judgement. Questioned in a BBC interview last month, Ruth Kelly, the Education Secretary, said that the commission's findings were not being accepted.
Sir David Normington, permanent secretary at the Department for Education and Skills, wrote to the commission saying that the DfES did not accept the report's conclusions. He called on the commission to think again and "set the record straight".
The commission, however, has so far refused to do so. Sir David Rhind, its chairman, wrote back to say that ministers should agree that improvements were less dramatic than the scores suggested.
In evidence to the commission, the QCA backed the findings of the largest study into national test standards-setting, carried out by Alf Massey, of the University of Cambridge Local Examinations Syndicate.
It found that the pass mark for KS2 English was set five marks too low in both 1999 and 2000 because the standard of the reading test fell. Therefore the gains in reading had been to some extent "illusory".
Tim Oates, QCA head of research and statistics, wrote: "The Massey report confirms that standards have risen, but not necessarily to the extent suggested by national curriculum assessment outcomes (test scores)."
He added that the Government needed to consider "problems" implied by the launch of a high-stakes assessment system in Texas in the 1990s. Results there shot up, but in other tests, pupils fared no better than previously.
Richard Alldritt, the commission's chief executive, is to meet DfES officials later this month to discuss the issue.
* League tables should be based on the performance of pupils over several years, the National Foundation for Educational Research is recommending in a draft report.
The NFER, in a review of educational statistics, also recommends that tables are not based on the percentage of children reaching a particular standard.