Ken Boston, chief executive of the Qualifications and Curriculum Authority, was responding to criticism that standards of written English in the two exams have deteriorated sharply.
Mike Tomlinson, who led an 18-month inquiry into new secondary qualifications, said last week that he found it "difficult to defend" the current practice in which poor spelling and punctuation were ignored provided that what was written could be understood.
Mr Tomlinson, the former chief inspector of schools, demanded an urgent review of marking procedures in all exams.
Dr Boston told The Independent: "We should reward good spelling and good grammar and the use of correct punctuation, and we should penalise errors.
I have no doubt about that because it is at the heart of good literacy."
The QCA maintains that examiners take standards of written English into account, but Dr Boston has the power to tighten the code of practice.
Dr Boston also said he would head a new committee that will meet fortnightly to check on planning for next year's national curriculum tests.
The move comes after a damning report on the administration of this year's key stage 3 English tests.
Charles Clarke, the Education Secretary, told MPs on the select committee this week that he agreed with the idea of deducting marks for poor spelling. "The question of those core skills is a key question for us to get right and address earlier rather than later," he said.