He told a conference that while teachers were getting better at their job, too much inconsistency remained in their subject expertise and knowledge.
He questioned whether a proliferation of advisers in areas ranging from the national literacy strategy to the Connexions service were providing a "focused and coherent" approach to professional development.
Mr Clarke cited figures from the Office for Standards in Education which compared the quality of lessons in different subjects between 19967 and 20023.
While overall the number of lessons judged to be very good or excellent at key stage 3 increased by 16 per cent over that period, there were marked differences between subjects.
History recorded one of the best improvements, with 21 per cent more lessons deemed very good or excellent. At the other end of the range the figure was just 8 per cent for design and technology.
Mr Clarke told the General Teaching Council for England conference in London that teachers deserved a "small pat on the back" for improvements but said: "Overall, the system is quite unreliable if you are a pupil or a parent.
"It's not quite hit and miss, but it's almost hit and miss whether your teacher is working rigorously and systematically to improve the classroom experience for every child."
He said a clear model had to be drawn up for professional development and improving teachers' subject knowledge. "I would prefer it if more pupils were being taught in classes where the teaching was good or excellent, as opposed to not good or excellent."
Mr Clarke conceded that funding crises in schools, such as those experienced last year, meant training was among the first items to face cut-backs. In a reference to the publication of the Children Bill last week, Mr Clarke said he hoped most schools would be extended schools providing a one-stop-shop for vulnerable families within seven or eight years.
He called on the GTCE to rise to the challenge of developing training structures that would "encourage professionals to work together on the needs of the child".
Chris Keates, deputy general secretary of the National Association of Schoolmasters Union of Women Teachers, said: "Teachers will be bemused and dismayed by his seemingly negative comments."