The plea came from Douglas Trickett, education director of the London borough of Hounslow, as local authorities finalised proposals for speeding up the dismissal of incompetent teachers.
Councils want to get rid of failing teachers in two terms instead of the current 18 months to three years.
The proposals agreed this week by the Local Government Association's education committee will go to Stephen Byers, the school standards minister, at the end of this month.
Mr Trickett told the LGA education committee there was no place for incompetent teachers in schools. But he added: "I do think a moment for a little bit of understanding and charity is needed. We have got to find an effective and efficient way of dismissing incompetent teachers but at the same time we have got to improve the climate in which our headteachers and teachers work.
"Morale is still low and if we are not careful all we are going to do is denigrate teachers. We don't want to get taken in on a witch hunt."
Churches, teacher unions, governors and local authorities are all being consulted by the Government on a "fast but fair" procedure for removing incompetent teachers.
Proposals put forward by the LGA include giving LEAs enhanced powers to veto the appointment of heads and to fire unsatisfactory heads. (It is understood ministers are looking at a different procedure for heads.) The LGA also suggests reintroducing a probationary period to weed out unsatisfactory teachers earlier.
Graham Lane, education chair of the LGA, said: "Sacking must remain the final recourse against teachers who do not make the grade. It is only the final recourse, and we will not be an excuse for schools not to give people the support they need to improve their performance."
Local authority officials said the proposals did not signal a return to the LEAs interfering in the day-to-day running of schools - it would be up to individual schools to appraise the performance of their staff.