This latest move in the clampdown on the controversial modular A-levels has caused outrage among the exam boards who believe their candidates are being picked out for unfair treatment.
Students hoping to improve by a grade could theoretically fail the whole exam if the re-sit goes wrong.
A spokesman for the School Curriculum and Assessment Authority this week confirmed that its interim advice to ministers is that modular candidates should stick to one re-take per section of their course. In addition, they must keep whatever final mark they receive.
He said there are no plans to extend the rules to standard A-levels - where everything is tested in a final exam - or to the modular GNVQ courses.
SCAA, which will make its final recommendations in December, is also calling for the standardisation of exam sittings across the different boards, with June and January common to all. He said that the current variations in exam time cause problems for school timetables.
The widespread introduction of modular A-level courses in English, maths and science two years ago has caused concern. Only 30 per cent of the marks are taken in the form of a final exam and some commentators claim that testing candidates as they go along gives them an unfair advantage.
The first batch of modular results came from this year's candidates and showed that the overall pass mark was higher than for traditional courses. The proportion reaching the top grades was however lower, as the exam boards were keen to point out.
The Education Secretary Gillian Shephard has already responded to the criticisms by promising to limit the number of re-takes - almost certainly to one per module.
The boards have vigorously denied that modular courses are easier. They claim that picking out A-levels for special treatment will undermine Sir Ron Dearing's report on 16 - 19 education and damage his attempt to boost the standing of non-academic qualifications.
"It is always GCSEs and A-levels that they pick on," said George Turnbull from the Associated Examining Board. "I really don't understand why. If a change is good in principle we should apply it to all exams. It's another step away from parity of esteem and equivalence of academic and vocational qualifications. "
"I don't see how parity of esteem can be achieved if there's a different set of rules for different sorts of exam. If there's a different set of rules then it's a different product at the end of the day."
Kathleen Tattersall, chief executive of the Northern Examination and Assessment Board this week told the Historical Association's annual conference that the new restrictions on re-sits would demoralise young people.
"We need coherence and consistency across the whole system. Will this principle apply in every other situation where re-takes occur?"