Candidates entered for the higher papers who fail to get a D do not qualify for an alphabetical grade while those who take the lower paper can get a C to a G.
But schools and exam boards have persuaded ministers to allow higher paper candidates who just miss a D to be awarded an E.
Exam boards now fear there could be chaos if schools take last-minute decisions to enter more pupils at the higher level. One science teacher said: "There will be many teachers who would have entered students for the higher paper if they had known it would cover grades A to E."
A GCSE Joint Forum spokesman said: "This is a positive step for those very few candidates who have been entered for an inappropriate tier. There is absolutely no need for any entries to be changed."
A Qualifications and Curriculum Authority spokeswoman said: "It is a safety net to protect the interests of a small number of candidates that was lobbied for by schools and examining boards."
Heather James, assistant chief executive of Northern Examinations and Assessment Board, said a review of tiering was needed.