And nearly 500 schools that are taking part in the pilot are likely to enjoy an advantage in league tables over those not participating.
Professor Paul Black, of King's College, London, is among a team of exams experts who have raised concerns about the alternative to Sats tests.
A two-year trial of the new tests in English and maths for 7- to 14-year-olds begins in 484 schools this term. They will be set at a single national curriculum level and pupils will take them whenever their teacher believes they are ready.
But Professor Black, who led an advisory group whose report for the Conservative government in 1987 paved the way for national curriculum assessment, said it would not offer reliable information on standards.
The new system raises the probability of "level inflation", Professor Black and five colleagues at the Assessment Reform Group said in a paper submitted to the Government.
Once a pupil takes one of the new tests and passes it, the level they achieve can never be taken away. Thus, an 11-year-old gaining level 5 in English could never be registered as below that level during secondary school.
Yet the paper highlights the fact that currently, in English, 3 per cent of pupils "regress" a level from key stage 2 to 3. An additional 4 per cent of pupils are absent for the KS3 English test, and so are counted as scoring zero in national figures.
Under the new system, the highest level achieved by any pupil by the end of KS3 would be counted. This would give both these groups of pupils higher KS3 test scores than they would achieve at the moment and raise national results by up to 7 percentage points.
Results will also rise because pupils will be able to resit the tests as often as they want with only the best scores counting. Other pupils will have just one chance at taking the Sats.
Professor Black said: "It is inevitable that if this system is widely used, standards will appear to rise even if pupils' actual performance has not undergone any real change."