Schools will always try to find ways to "game" the exams system to boost results, Michael Gove has said.
The Education Secretary suggested that the Government needs to anticipate how this will happen in an attempt to stop it.
Giving evidence to the Commons education select committee, Mr Gove said that schools are still playing the system.
There are "two different types of gaming", he said.
"Some schools are choosing exam boards in order to get an easier pass, others are choosing particular combinations of subjects," Mr Gove said.
In some cases, schools are choosing qualifications that they believe will be easier for their pupils to pass, while others pick tougher combinations such as physics, maths and chemistry.
"With almost all accountability systems there is a danger, over time, that people learn how to play the system, so we have to try and anticipate how they will do that," Mr Gove said.
Under the current accountability system, schools are judged on how many pupils score at least a C grade in five GCSEs, including English and maths.
Mr Gove also clashed with MPs after refusing to disclose the concerns that England's exams regulator Ofqual has raised with him about the Government's plans to axe GCSEs and replace them with new English Baccalaureate Certificates (EBCs).
He told the select committee that Ofqual's chief regulator Glenys Stacey had written to him, but refused to give details, telling them they would have to ask Ms Stacey.