Dr Nick Tate's comments were made at a special briefing for The TES following widespread allegations of "negative" marking and "unfair" low levels (grades) in the national curriculum English tests for 14-year-olds.
This year the tests were marked by external markers for the first time, and the scripts returned to schools for checking.
Dr Tate, the chief executive of the School Curriculum and Assessment Authority, said: "When we decided to go down the road of openness and accountability in returning scripts, we did so because we thought it very important indeed . . . that people should have a chance to look at how the marking had been done and tell us if there were problems.
"I think it was a bold move to do that. New Zealand is the only country which has done this and it is a very small country so what we have done in terms of the size of this country is a world first.
"I am not surprised there are a number of problems . . . we are in the middle of a review."
There will be no formal investigation into what teachers have called "a farce" and "a national scandal" but the council will, as a matter of course, evaluate the results of the tests, and consider all the complaints. They will be looking at quality of marking and paying English extra attention.
But Dr Tate stresses that the English test appeals to the exam boards were so far only 0.5 per cent of the 5,000 key stage 3 schools while 5 per cent of schools (250) have made telephone complaints to boards. He says he is not surprised by the figures, since the system is in its first year.
There were 600,000 scripts and 2,300 markers, he said. It was inevitable that no matter how thorough the training of the markers, and how careful the supervision, some markers would slip through the net.
Mike Kingdon, manager of external marking for the London Examinations board's London and East Anglian region, said 40 per cent of the calls the board had received were about markers' adding-up errors; the remaining 60 per cent were split between complaints about how the scripts had been marked and "general problems".
Mr Kingdon was unwilling to be more specific than that although he did say that the calls followed no particular pattern - unlike the calls to The TES which have all been concerned with "rigid" and "unfair" marking, particularly as it affected the brighter pupils.
Markers only received one day's training, but Dr Tate said that this was "thorough and went well". Chris Jones, a SCAA assistant chief executive said the exam boards had done a lot of work to "weed out" substandard markers before the training stage.
The markers were taught to mark to the mark scheme and given information about the rationale behind it. Part of the training involved looking at how 2, 500 pupils had answered the national test questions in English test trials.
Many of the callers and letters to The TES were concerned about the link between the national test results and GCSE performance. Both key stage 3 and 4 are assessed against the same statements of attainment in the national curriculum, they say. Mr Jones said no direct link could be made between the two because the GCSE was introduced before the national curriculum and had its rules.
But Dr Tate conceded that the link between the tests and GCSE was "an interesting point which requires further consideration".