Boris Johnson said it was an "interesting fact" that the UK has "some clerical fossils still in our legislature".
Speaking on LBC Radio he said the separation of Church and state is "not perhaps as thoroughgoing in this country as you might like to think".
Twenty six bishops of the Church of England sit in the House of Lords. Known as the Lords Spiritual, they read prayers at the start of each daily meeting and play a full and active role in the life and work of the Upper House.
The Archbishops of Canterbury and York and the Bishops of London, Durham and Winchester are automatic members of the House of Lords.
The remaining 21 places on the Bishops' Bench are given to those that have served the longest.
Mr Johnson was responding to a question about the use of Sharia law courts opening in the UK.
"Everybody must be equal under the law, and everybody must obey the same law. That is absolutely cast-iron," he said.
He added: "I'm worried sometimes by the faint bat-squeaks of support that I hear for that idea even from clerics in the Church of England.
"I take grave exception to some of the support I see sometimes - and from clerics in the Church of England who've come out in favour of this, I've noticed, and said we should be a little bit indulgent of this.
In 2008 Former Archbishop of Canterbury Rowan Williams said it may be "inevitable" that elements of Sharia would be incorporated in British law.