Heads with many transient children are concerned that they cannot produce viable targets as there are no national benchmark figures to enable them to compare themselves with similar schools.
Turbulence - as high pupil turnover is known - particularly affects inner-city schools and those which serve the 85,000 children from families in the armed forces.
Some high-turnover schools are compared - often unfavourably - with others that have similar levels of poverty but a more stable pupil population. However, the Government's benchmarks are unlikely to be revised.
The problems facing the headteachers and governors of such schools were acknowledged by Ralph Tabberer, of the DFEE's standards and effectiveness unit at a conference organised by the Association of State Schools for Service Children.
"It's difficult where you have got very high turbulence," he said. "How can you use benchmark data when you have service children who don't have free school meals? And how can you use teacher forecasts when two years ahead it's going to be almost a different class?" he said.
"We accept it is almost impossible. But we don't want you to walk away saying targets have no point. We must not accept that because there are difficulties pupils are going to be at the low end of performance. If you drop your expectations, the children will fail."
According to a survey carried out by the association, several schools say turbulence figures - showing the percentage turnover of pupils each year - should be used for benchmarking schools, rather than free school meals.
An Oxfordshire primary noted how its free school meals indicator put it in the upper reaches of the benchmarking tables. But 60 per cent of the pupils taking key stage 2 tests had not been there for key stage 1. Another, in Gloucestershire, said half of its pupil population changes every two to three years. "You can only use local pupils for targets," it adds.
The challenges posed by transient pupil populations were also acknowledged in this week's Government report on improving the lot of inner-city schools, Excellence in Cities.
The DFEE has commissioned research on the effects of pupil turbulence, and a report from Janet Dobson, of University College, London, is due to be published in July.
Dr Dobson, who also spoke at the Colchester conference, has identified several highly mobile groups - including refugees, travellers, forces children, and the "mobile poor". London has the biggest turbulence problems, with evidence from education authorities around the country that mobile pupils do less well than their more settled classmates.
Excellence in Cities, 6