Larry Flanagan criticised how some journalists and politicians "portray a problem as a crisis".
He told the EIS annual meeting in Perth a "more considered analysis" would be useful.
Mr Flanagan spoke as delegates confirmed they may take industrial action unless their pay improves.
The union's general secretary said some teachers were fearful that in the run-up to next year's Scottish election, politicians may seek to overplay concerns to score political advantage.
Mr Flanagan said there were also misgivings about the way some popular newspapers covered education, believing they sensationalised problems but did not reflect the reality of the situation in many schools and classrooms.
Addressing delegates, Mr Flanagan said: "It has been interesting to read recently some right-wing commentators having a specific go at the EIS, with one demanding that the first minister should 'take on the EIS'. But on what basis?
"The inference which might be drawn from these comments is that somehow the EIS is the block to 'progress' however that is defined - when the reality is that as Scotland's teachers, we are the vehicle of progress."
Mr Flanagan said no-one was suggesting "that everything in Scottish education is perfect - clearly it isn't".
But he said the union was "well aware of the attainment gap" and was working jointly with the Scottish government on issues regarding child poverty.
A motion calling for a back-dated pay rise was backed overwhelmingly at the conference.
However, any ballot on industrial action is still some way off.
Moving the motion, David Baxter from Dundee said: "A restorative pay rise will boost the economy and is needed to give public sector workers the same spending power they had before austerity and pay freezes and sub-inflation level pay awards."
He added: "Teachers are working, on average, 46.5 hours on a contract that pays them for working 35 hours.
"Teachers are being worked harder, paid less and are being seriously under-valued.
"Teachers have had enough. This is the time to act."
Seconding the motion, Mike Callaghan, from Angus, said: "If we do not take action now, after at least five years of pay erosion, when will we?"
Teachers' pay is negotiated nationally through a joint body which involves unions, councils and the Scottish government.
The head of Scotland's biggest teachers' union has warned that education should not be used as a political football by critics.