The Church of England has defended a tweet saying it was praying outspoken atheist Richard Dawkins, who has had a stroke.

The tweet read: "Prayers for Prof Dawkins and his family" after the Oxford professor announced he had had a "minor stroke". However the Church's communications director, Arun Arora was forced to defend the tweet after it was accused of mockery and "trolling".

"It was a genuine tweet offering prayer for a public person who was unwell," Arora wrote on a blog post.

The eminent biology professor and author of 'The God Delusion' cancelled a tour of Australia and New Zealand after being rushed to hospital on February 5. 

Dawkins has since said he is recovering well and is "getting much better".

"It's not too bad. I'm very grateful to everybody who has been sending me good wishes from all around the world," he said in a audio update on Soundcloud.

The announcement of Dawkins' stroke prompted a Twitter storm over whether or not to pray for him. A number of Christians said they would but many supporters urged people not to pray for him. 

"The prayer tweeted on Friday evening was for Richard Dawkins.

"It's hardly surprising that I don't agree with all of his views. But there is a danger of reducing him to a one trick pony. His views are more nuanced than both supporters and detractors would usually acknowledge...

"I wish Professor Dawkins well. I hope he makes a swift and full recovery and wish him the best of health. I will pray for him too. It is the very least I can do."