Three-quarters of all complaints made by headteachers to the General Teaching Council of England are rejected, according to Government figures.
Responding to a parliamentary question posed by the Liberal Democrats, schools minister Vernon Coaker revealed that 315 out of 419 referrals made by headteachers are dismissed without any further investigation.
The numbers also show that the GTC takes at least three months to investigate a complaint, and more than a year to conclude a case if it goes to a hearing.
The Lib Dems said they were "concerned" by the figures, adding that it places major question marks over the efficiency and effectiveness of the quango.
Lib Dem education spokesman David Laws said: "These figures will not inspire the confidence of headteachers considering making a referral to the GTC.
"There are many excellent teachers in our schools but it's important that the system can properly manage those situations where teachers fail to meet expectations."
Mr Laws demanded that the GTC explain why so many complaints are being rejected and that it should consider ways of speeding up investigations.
"The time taken by the GTC to make its investigations is very concerning. Most appear to take over six months and many take over a year. This is not only very disruptive but is presumably incredibly costly, too," he said.
Shadow schools secretary Michael Gove said: "The GTC is clearly an inadequate body for the hugely important role it carries out, but in the case of investigating complaints about teacher competence it wouldn't be necessary if heads had proper powers to hire and fire their staff.
A GTC spokesperson said: "Around half the cases referred to the GTC involve minor one-off convictions or cautions that do not raise questions about whether a teacher should be allowed to stay in the profession.
"That is why the number of rejected referrals appears high. It is important that GTC takes a proportionate approach to one-off offences that occur outside the workplace."