The league tables from last year's tests remain unpublished
Further concerns have been raised about the marking of English "Sats" tests taken in England's secondary schools.
The new exams watchdog, Ofqual, has reported that the quality of marking in last year's national tests was "at least as good as in previous years".
But it said research into the marking of the English tests taken by 14-year-olds would, if representative, give "significant cause for concern".
The body which develops the tests, QCA, says that study was not representative.
A sample of hundreds of papers found wide variation in the marking of English tests at Key Stage 3 (age 14).
In 44% of cases, papers did not end up with the grade an expert panel of examiners would have given it.
The QCA (Qualifications and Curriculum Authority) says the "assessment" was not a direct indication of the quality of test marking nationally.
In a statement, it said: "The findings of all of the work carried out by QCA over the last three years suggest that there are high levels of accuracy in maths, science and short English questions.
"Other English test questions require an extended narrative response, rather than a right or wrong answer, so markers have to exercise their professional judgement to a greater extent.
"The range of divergence between different markers will be greater as a result, in line with findings from other national and international studies."
One of the authors of the report, Jo-Anne Baird from Bristol University, told BBC News: "This gives us some information about the quality of the marking but the figures are not entirely reliable because the data came from operational marking checks and might not represent the whole picture."
Ideally, she said, a sample would be taken from the whole pool of examiners and papers. However, the study, which looked at science and maths papers too, had involved thousands of examiners.
'At least as good'
Ofqual said its "final judgement" about the quality of marking of national curriculum tests, based on its own monitoring, evidence and the QCA's reports, was that "the quality of marking in 2008 was at least as good as in previous years".
Anecdotally, questions had been raised about the quality of the marking during the uproar about delays in the marking of papers.
Record numbers of appeals for remarking were made.
The delays led to the sacking of the company which had the marking contract - ETS Europe - and criticism of the QCA.
Ofqual's chairwoman, Kathleen Tattersall, said: "A number of measures were introduced last year to try to improve marking quality. The impact of these measures is unclear, but it is important that marking quality initiatives continue to be used.
"While there was a rise in the number of review requests in 2008, Ofqual's own research shows that test review information alone is an unreliable barometer of test marking quality."
On the English marking at Key Stage 3, she said: "If the studies reflected the quality of marking in live tests then in maths and science this would suggest that the marking quality is reasonable but we would be concerned about some of the findings for English marking at KS3.
"The high level of misclassification in English suggests significant cause for concern.
"There are always likely to be difficult issues around the marking of subjects like English, particularly with extended written answers, and the report draws attention to the impact that those problems have on the classifications in English tests at Key Stage 3."
At the height of last year's furore over the marking of Sats papers, the government announced that 14-year-olds would no longer sit national tests which were marked externally, but would be assessed by teachers.
Shadow Schools Minister Nick Gibb said: "This is an issue of competence and complacency. The government presided over a complete breakdown of the sats marking system last summer and now, despite record levels of school dissatisfaction with the quality of marking, government officials are saying standards are fine.
"This is just part of the larger problem of the government devaluing our curriculum and exam system."
The results of the reviews (appeals, in lay terms) have also been published.
They show that at Key Stage 3 (14-year-olds) in more than half (56%) of cases where individual re-marks were requested, a higher grade was awarded.
That compares with figures of 44% for 2007 tests and 38% for those of 2006.
At Key Stage 2 (age 11), there were more than 25,000 requests for English papers to be re-marked (there were 14,500 the previous year). In one in six of those cases, a higher grade was awarded.
A record number of individual appeals was made for English at Key Stage 3 - more than 11,000, compared with 3,400 the previous years.
Requests for re-marks in maths and science also leapt.
Schools Minister Sarah McCarthy-Fry admitted it was likely that the increase in requests for reviews had been due, "in large part", to last year's failures.
She said: "Given delays over the summer, it is no surprise that some schools had concerns about their results. The contractor who was delivering the test has since had its contract terminated.
"Whilst it is an important part of the quality assurance process that schools are able to request reviews if they have concerns about marking, Ofqual advise that the quality of marking in 2008 was at least as good as in previous years.
"The overall proportion of review applications is very small when compared with the number of pupils taking the test."