The School Curriculum and Assessment Authority has written to schools outlining the procedures.
Sir Ron Dearing, chairman of SCAA, said: "While it is clear to me that the vast majority of schools administered the tests fairly and professionally, I do take these concerns very seriously. The purpose of these changes will be to ensure, and thereby reassure the teaching profession and parents, that the tests are carried out fairly and consistently across the country."
Meanwhile results of a survey by the National Association of Schoolmasters Union of Women Teachers of its members in more than 1,000 primary and nearly 700 secondary schools show that more than half thought test guidelines were clear and helpful. Four-fifths found there was a close match between the recorded test and teacher assessment results, but a quarter reported that the tests and teacher assessment had created an excessive and unacceptable amount of additional work.