Pickles changed the law in 2012 to ensure that English parish councils could not face legal challenges for including prayers in public meetings, and accused the last Labour government of "diminishing Christianity" by suggesting that religion and politics could not mix.
The minister told delegates at the Conservative spring forum in London that non-believers should not be able to impose "politically correct intolerance" on others.
"I've stopped an attempt by militant atheists to ban councils having prayers at the start of meetings if they wish," said Pickles. "Heaven forbid. We're a Christian nation. We have an established church. Get over it. And don't impose your politically correct intolerance on others."