Mr Whannel won a prolonged standing ovation after delivering a scathing rebuttal of the media-driven campaign against the clause that bans the promotion of homosexuality in schools.
"They've tried to create an artificial danger and then suggest measures to try to prevent this danger. There is no danger from gay rights people, gay rights teachers or any teacher as regards sexuality. It's a bit like the Nazi conspiracy against Jews, bankers andCommunists which was used in the 1930's to promote the Nazi party," he said.
Mr Whannel described the Cardinal's statements as "particularly disgraceful and reprehensible" and as an "appalling indictment of his own personal view".
The Cardinal had described the gay community as a perversion but "there is no greater perversion than the incitement of hatred", the head said.
Mr Whannel said it was not the job of schools to promote any kind of sexuality. But a large number of teachers had already complained that the existence of Section 2A had inhibited their teaching of sex education.
Delegates overwhelmingly backed the union's pro-repeal stance.