Nigel de Gruchy, general secretary of the NASUWT, said he was actually complimenting them for raising standards when he used the phrase.
He told the BBC he was arguing that greater responsibilities for classroom assistants meant they must be suitably qualified and trained and "could not be, as I used the phrase, 'pig ignorant peasants'".
A row had broken out over reports of Mr de Gruchy's comments and Unison general secretary Dave Prentis said he was "appalled" by the "outrageous" phrase.
But Mr de Gruchy said his intended meaning had been misinterpreted.
'No comparison'
He used the phrase when speaking at a Social Market Foundation debate, shortly before Education Secretary Estelle Morris was due to make an address about classroom assistants.
He told BBC News 24: "I was warning the government about a mistake that it might make in the future, I was making no comment whatsoever about the quality of classroom assistants."
Mr de Gruchy claimed he had not meant to cause any harm or offence and was "more than happy to offer my apologies to any classroom assistant" offended by the remarks.
The NASUWT, he said, was one of few unions happy to look at extending the role of people like classroom assistants to take the pressure off teachers.
He said: "I simply said that we had to be careful to make sure that whatever roles we developed we had to make sure that we appointed appropriately qualified and appropriately trained people to such roles."
The government is concerned about a shortage of teachers, expected to reach 40,000 posts in five years, and is keen to see schools staffed by adults with a "range" of skills.
Mr Prentis said classroom assistants had been compared to a "teacher's life support system" and added: "I believe that Nigel de Gruchy is totally out of touch with reality".
"Classroom assistants have a wealth of experience and play a vital role in educating our children," he said.
A spokesman for the Department of Education and Skills said: "The government values and respects the work of our 186,000 teaching assistants and support staff."