The chief executive of exams watchdog Ofqual was in Bury St Edmunds on Friday to meet with Geoff Barton, headmaster of King Edward VI school.
Last summer thousands of pupils missed out on Grade C English GCSEs after changes, backed by Ofqual, to the marking boundaries.
Mr Barton who has spoken of the injustice of those changes, said: “What happened almost had an inevitability because of the way qualifcations had been designed.”
Mrs Stacey said those changes, which saw English become more modular, and moved from two to three qualifications, were to improve standards.
“It is easy with the benefits of hindsight to see how it could be designed differently,” she said.
She is now talking to heads about exam changes to come in from 2017.
“This is about taking GCSE and making it the best it can be, giving students real skills that will see them through life rather than jumping through hoops,” she said.