The Home Office letter was met with widespread disbelief and consternation after excerpts were published to Twitter by the asylum seeker's caseworker, Nathan Stevens.
The claimant said in his application that he had found "peace, forgiveness and kindness" in Christianity in contrast to the "violence and revenge" of his former Muslim faith.
An official in the Home Office challenged his interpretation, though, and quoted several passages from the Bible to refute his claim, including Matthew 10:34 where Jesus says, "Think not that I am come to send peace on earth; I came not to send peace, but a sword."
The official then cited Revelation 2:22-23 and chapter 9:3-6, stating, "Similarly, the book of Revelation is filled with imagery of revenge, destruction, death and violence."
The official added: "These examples are inconsistent with your claim that you converted to Christianity after discovering it is a 'peaceful' religion, as opposed to Islam which contains violence rage and revenge."
The Home Office responded at the time by saying that the letter was inconsistent with its policies and that it was working with faith communities to improve its guidance and training.
Church of England Bishop the Rt Rev Paul Butler was among those to have expressed outrage about the letter, saying that the use of the Bible quotes represented "such a profound misunderstanding of the texts and practices of faith communities" and that the management structures and ethos of the Home Office needed "serious overhaul".
In the House of Commons yesterday, Tory MP Sir Edward Leigh questioned the Home Secretary on what was being done in response to the letter.
He asked Mr Javid whether he would acknowledge that "amongst his officials, they may be so worried about being accused of Islamophobia or anti-Semitism that they overcompensate by becoming Christian critical and they don't understand that Christianity is the cornerstone of all our freedom".
"I found the letter totally unacceptable," he said.
"It is not in accordance with policies at the Home Office in any way. I have ordered an urgent investigation and not ruled out any further action."