They have embarked on a fact-finding mission to see if schools policy could be improved.
A Treasury source said they were acting independently of the DfES over concerns that, despite improvements among brighter pupils, many with lower abilities were leaving school with few qualifications.
It is not the Treasury's first foray into education policy. Last September it led an inquiry into enterprise education in schools and has kept close control over spending through public service targets.
The Treasury study may inform future decisions about how much funding the DfES should get and under what conditions.
But the move into schools has been criticised by headteachers' leaders.
John Dunford, general secretary of the Secondary Heads Association, said:
"We have already seen Gordon Brown intervening in education beyond the limits of a purely funding brief and I do worry about this.
"I think the inevitable consequence is that their policies are not properly joined up with those of the DfES and that we end up with a spate of unwelcome Treasury initiatives.
" My message to Gordon Brown is, 'Leave it to Charles.' " Eamonn O'Kane, general secretary of the National Association of Schoolmasters Union of Women Teachers, agreed that the Treasury's involvement in education was part of a worrying trend.
"The education policy of this country should be the responsibility of the education department," he said. "The omnipotence of the Treasury has to be challenged."
Gerald Imison, joint acting general secretary of the Association of Teachers and Lecturers, said: "The ATL has always been concerned that there are far too many government initiatives on education.
"If other departments are going to start getting involved then this is a recipe for absolute disaster."
In an official statement the Treasury confirmed its interest in the effect of education on productivity, but it denied that it was working independently of the DfES on the issue.