Schools are entering teenagers for GCSEs early, or multiple times, in order to secure good grades, the regulator has warned.
Tens of thousands of pupils took papers for more than one maths GCSE last summer, while the numbers sitting key English and maths exams before they are 16 has soared.
It also indicated that high numbers of pupils sitting exams early could affect this summer's GCSE results, which are published next month.
The watchdog's figures show that around a quarter of maths GCSE entries (23%) this year, along with one in 10 English and English Language GCSEs (11% and 10%) are for students who are aged 15 or younger, effectively pupils who are sitting papers earlier than the final year of secondary school. This is a rise on last year.
At the same time, the number of young people being entered for IGCSEs in maths and English - seen by some as a tougher alternative to GCSEs - has also risen.
And around 15% of students taking maths GCSE last summer - about 90,000 youngsters in total - also sat at least one paper from a second maths GCSE, Ofqual said, adding that these students "tend to be concentrated at the grade C/D border".
Chief regulator Glenys Stacey suggested that multiple entries are being used as a "tactic" to help students gain a C grade, and that there is a "fine balance" between doing the best for a pupil and demotivating them.
"We do think as well that this is more common for students that are judged to be at the C/D boundary, the evidence is that's what we're seeing. We're not suggesting that this is happening for students of all abilities. But where a student is at risk, perhaps, of not getting that precious C grade then a tactic is to enter the student for more than one of the qualifications and either take a view or ride both horses to the end.
"In some cases we're seeing, in maths, that students are riding two horses and then moving to a third horse, a completely different one, halfway through."
She said there were "questions to be asked" about the educational value of this for a student.
"Students obviously need the best possible outcomes and, particularly, they are looking for a C grade or above in English and maths, they are so critical to the future of those students, their life chances are very affected by those. One can understand every legitimate effort a school might make to a get a student those grades. One would hope that involves teaching them as well as possibly a lot of assessment," Ms Stacey said.
"The issues really in terms of the ethics of this are fairly plain. There's a fine balance between doing the best for a student by perhaps putting them in for more than one assessment and demotivating a student by putting them through a good number of assessments when actually, perhaps, the time might be better spent teaching and preparing the student for one assessment."
Ms Stacey acknowledged that the pressures of league tables could be playing a part, saying that this issue made the awarding of GCSE English last year "enormously difficult."
"We had a qualification there that was weak in design, it was not resilient to those pressures and it did affect confidence and the rest of it, we know that," she said.
"We've no reason to believe those accountability pressures have lessened over the last year, not at all."
Government plans to overhaul league tables and move away from the five A*-C grades at GCSE measure are encouraging and could help lift the pressure off the C grade threshold, Ms Stacey suggested.
Ofqual also said that the controversy over last year's GCSE English results - which saw headteachers argue that thousands of teenagers received lower than expected grades after grade boundaries were moved - could be fuelling the switch to IGCSE.
In English language, the numbers taking IGCSE have risen from 18,000 last summer to 78,000 entries this year.
"The rise that we've seen over the last year has been significant, and it has been particularly in English. That would suggest to us that people are reacting to GCSE English last year," Ms Stacey said.
"There will be a good deal of uncertainty in schools about what to expect in GCSE English, I understand that, and so that would promote other alternatives."
The rise in early entries could have an impact on this year's overall GCSE results, particularly in maths.
"If you look at early entry in maths, 23% of those taking maths GCSE this year are Year 10," Ms Stacey said.
"If all of those students are really bright and able and more than ready to take a maths GCSE then we're going to see some pretty impressive results. If, on the other hand, the majority of those students are not full mature in their understanding of maths and are taking that qualification early to see what they can get or so they can get it out of the way and concentrate on some other GCSEs then we are going to see a different profile of results.
"We don't know at the moment, in that 23% whether they're all bright and able or whether they're all taking a shot at getting a C."
Ofqual has also acknowledged that it is expecting a "small drop in achievement" in GCSE science subjects this year, following changes to the courses.
The qualifications were toughened up in the wake of an Ofqual report in 2009 that found the courses were too easy. This is the first summer that the grades will be awarded for the new tougher courses.
The standard of the qualifications is more challenging this year than last, Ofqual said on Thursday.
Ms Stacey said: "We are expecting a small drop in achievement, that means that the level of demand in the specification is a bit higher, the assessment should be better, therefore a student needs to be well taught and well prepared to do well in that. So we are expecting a small drop in achievement."
Christine Blower, general secretary of the National Union of Teachers, said: "Ofqual's decision to pre-empt this year's GCSE results with a long explanatory note points to an examination system which is needlessly complex and difficult to navigate.
"The current GCSEs are fit for purpose and have proved to be popular both with students and their parents. The case has never been made for wholesale reform of GCSE examinations, or that standards are falling. Quite the contrary."