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Secularists have condemned the leader of Britain's evangelicals as "unChristian" after he accused them of exhibiting intolerance of his religious views.

The National Secular Society has attacked Dr Joel Edwards, leader of the Evangelical Alliance, for remarks made at the end of an address by Chief Rabbi Dr Jonathan Sacks on the need for religious tolerance.

The row gives just one insight into the future difficulties of enforcing legislation against incitement to hatred against homosexuals and against incitement of religious hatred.

Dr Edwards, who has been appointed a commissioner on the newly-formed Equality and Human Rights Commission, has been accused of making a career out of "opposing equality for homosexuals". After news of his appointment emerged, secularists described his organisation as "one of the most homophobic in Britain, sheltering extreme anti-gay groups."

After the Chief Rabbi finished his address on the need for religious tolerance, Dr Edwards said: "These groups have perceived that I am so intolerant that they will not tolerate my place on a body negotiating the choppy waters of 21st century tolerance.

"The timing could not have been more perfect. These comments go right to the heart of the debate that we are launching with Dr Sacks’ address: where does religious conviction fit in to society’s balance of rights, responsibilities, diversity, equality and multi-culturalism? The secularist would of course answer 'it doesn’t', but this would be to betray history. As Dr Sacks has so brilliantly said, the roots of liberalism and the new found tolerance that went with it were in fact religiously inspired."

Only a few weeks ago the Evangelical Alliance was among the organisations that celebrated 360 years since the Putney Debates, which pioneered the liberal democratic settlement, where the Levellers called for equal rights irrespective of status or property, although not gender. Dr Edwards said: "It was to Genesis and the Gospels that they turned to justify their demands. "

And some of the Levellers' prayer meetings lasted for five hours, which in the Jamaican Pentecostalism from which Dr Edwards has emerged would be referred to as The Preamble.

Dr Edwards said: "To remove religious conviction from the public square is as sensible as removing the engines from an aircraft in flight. For a while the plane may glide and to all extent seem fine, but before long the altimeter will only be headed in one direction, by which time it is too late to start remembering how it was you got airborne in the first place.

"A tolerance which calls for the removal of conviction is no tolerance at all. If modern day politics seeks to silence or exclude voices, be they religious, gay or atheist, then a key pillar of an open society will have been destroyed and we will be the poorer for it. It is our task in this debate to persuade society that tolerance is not the absence of conviction, or even of conversion. It is the absence of coercion. In a liberal democracy it is more intolerant to disallow religious views based on secular prejudice: after all, secularism is just another religious position."

Keith Porteus-Wood, of the National Secular Society, told The Times that Dr Edwards' remarks were not an accurate reflection of what is going on and accused him of being "unChristian" in his attack on secularism.