A technical report setting out methods by which standards in A-level physics, for example, could be compared with languages, English literature and other subjects will be published next week.
Modern linguists and physicists have long complained that their exams are harder than others.
Speaking at the Qualifications and Curriculum Authority's annual review, Isabel Nisbet, interim chief executive of the new regulator to be known as Ofqual, would not say which subjects were the hardest. Neither would she reveal whether judgements on subject difficulty would be used in setting exam grade boundaries.
It is a difficult task. An independent report in 2004 said no country had managed to do so effectively. Ms Nisbet said she would set up a public debate on subject difficulty in the autumn.
But she added: "We won't be trying to suppress debate, but will be trying to shine a light on the debate."
Ofqual, which is separate from the QCA, will start work in shadow form in April.
Speaking at the same conference, Mick Waters, head of curriculum at the QCA, said the accountability regime of league tables and targets held back some schools.
"The accountability framework inhibits some schools in the way that they work," he said.
Some schools wanted to develop new curriculum practices, but the pressures of preparing for tests made it difficult, he said. "In some places, (schools) over-practise testing before the tests, just in case, when the tests come up, they have not practised enough," he added.
His comments stand in contrast to those of David Bell, permanent secretary at the Department for Children, Schools and Families. Mr Bell told a parliamentary committee two weeks ago that it was unusual to go into a school where test preparation took up much of pupils' time.
Mr Waters' comments came after his colleague David Gee, managing director of the National Assessment Agency, said pupils were not over-tested.
Earlier, Sir Anthony Greener, QCA chairman, offered thinly veiled criticisms of the Government for introducing a string of changes this year.
He said the division of the former Department for Education and Skills into two new departments last summer had created uncertainty, while moves to create Ofqual and to move the QCA's base to Coventry were difficult to manage.