Victoria's Deputy Premier, Peter Ryan, is backing a campaign to have the Church of Scientology stripped of its tax exempt status.

Independent Senator Nick Xenophon has been leading the push to overturn the church's formal recognition as a religious body.

Mr Ryan says he does not agree with the Melbourne Lord Mayor Robert Doyle's decision to attend a Scientology function on Saturday.

Mr Doyle was the guest speaker at the opening of the church's new headquarters in the Melbourne suburb of Ascot Vale.

Mr Ryan says he is "opposed" to the organisation.

"As a general principle, there should not be a tax free status available to a church entity which is not, in fact, a church," he said.