Assessment advisers in several authorities say initial feedback from many schools indicates that the results have fallen below expected levels of achievement identified by their teachers, causing widespread unhappiness with standards of external marking.
They fear the poor key stage two results will concern parents who were expecting their children to do well based upon teacher assessment - a process which schools claim to be a much more reliable and accurate system for charting pupils' performance.
The latest wave of criticism, coming a week after hundreds of schools returned English scripts from 14-year-olds to the examination boards complaining of unfairness and rigid marking, has reinforced doubts over the credibility and the reliability of external marking.
Earlier this month the School Curriculum Assessment Authority launched an inquiry into allegations of cheating at key stage 2 in five schools. It has now written to their local authorities asking them to investigate the matter further.
A SCAA spokesman said: "We have also asked external markers to notify the exam boards if they feel unhappy about the scripts. If they feel further examination is necessary, they are referring the matter to us. So far we have contacted two headteachers requesting information about the circumstances in which the tests took place."
David Hanson, past president of the Association of Assessment Inspectors and Advisers and an assessment adviser for Wiltshire, said the latest English results showed: "Either the marks scheme is not properly aligned to the levels or the interpretation of the marks scheme is being too rigidly applied. It is for the examination groups managing key stage two and three to get their house in order."
But while the English results were poorer than anticipated attainment levels in science were significantly higher than many schools had expected.
Mr Hanson said: "The high results in science will create a problem further down the road. One level is equal to two years' maturation of the child's learning, so, later on, key stage three children may appear not to have made much progress when in fact they have. I believe we may have a problem waiting in the wings."
Carola Garvie, Hertfordshire's assessment team leader, agreed. "Time will tell, but the evidence to date does not lead professionals to believe external marking is the most reliable model, but rather the converse," she said.
"External marking has meant many headteachers or teachers have spent hours collating, packing scripts to send to markers and then had to remark them when the results did not reflect the anticipated attainment level for some pupils. "
Headteacher Marian Manger launched a stinging attack upon the credibility of external marking when KS2 English papers were returned unchecked to Oakham Church of England primary school in Rutland, Leicestershire.
She said: "We submitted papers from 44 children. There is a line at the bottom of each paper which should be signed by the external checker. None of them were signed so we have no proof they were checked at all.
"Furthermore, one of the four sheets with the final level results was not completed so I had to work this out from the raw scores. The marker has not done her job properly and we are not satisfied that the results are accurate.
"But when I rang the Midland Examining Group external marking department I was told to assume the checker had forgotten to sign the forms. I consider this to be a disgraceful inefficiency and a waste of money on markers who are not earning their fees."