Dawkins, a distinguished evolutionary biologist at Oxford, is one of the world's leading voices for secularism, and a fierce critic of religion.
When news broke Friday that the 74-year-old had suffered a minor stroke, forcing him to cancel scheduled appearances in Australia and New Zealand, the Church of England retweeted a report of his condition with a statement offering "prayers for Prof. Dawkins and his family."
The remark proved divisive on Twitter, with some describing it as insensitive given Dawkins' widely known disdain for religion.
Former British politician Nikki Sinclaire asked whether the church was being "sarcastic or ignorant," while Scottish politician Murdo Fraser commended the church for "top trolling."
But others thought the criticism of the tweet was unwarranted. One user responded to Sinclaire by arguing that praying for someone "causes them no harm or disrespect," and pointing out that the church was merely wishing Dawkins well.
'Misunderstanding of prayer'
The Church of England's communications director issued a statement Saturday
in response to the controversy, saying criticism "stemmed from a misunderstanding of what prayer is."
The statement, from Rev. Arun Arora, pointed out that Dawkins' views "are more nuanced that both supporters and detractors would usually acknowledge," citing a recent example where the scientist had criticized UK movie houses when they refused to screen a commercial featuring the Lord's Prayer.
"I hope he makes 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," Arora's statement concluded.
He had spent four days in hospital, but had since been discharged. He said he had suffered a hemorrhagic stroke, which would affect his coordination, but not his "higher cerebral function, thank goodness."
"I gather if you've got to have a stroke, this is a pretty good one to have," he said, adding that the biggest challenge he had encountered was "buttons."
"You forget what a fantastically precise instrument the human hand is," he said.