Conservative MP Lucy Allan has accused the Archbishop of Canterbury, Most Rev Justin Welby of "alienating" Church of England congregants by taking a "strong political stance" on issues such as the Rwanda policy.
Ms Allan was replying to an earlier tweet by Archbishop Justin in which he set out the reasons for opposing the Rwanda policy.
The head of the Church of England said the Church opposed the policy because it "outsources our responsibilities, and treats vulnerable and traumatised people without any kind of dignity, compassion or justice."
He had also previously described it as "ungodly" and "immoral".
But in a tweet, the MP for Telford asked the Archbishop if people with different political views were welcomed in the Church: "When the Church takes a strong political stance, it forgets that many of its congregation, who do not share its view, will feel alienated and unwelcome. Is a Conservative welcome @JustinWelby in the Church of England?"
The Archbishop then replied to Ms Allan's tweet saying: "We're making a moral point based on our belief that every person is made in God's image, and the calling from Christ to love our neighbour.
"For that same reason, yes absolutely - everyone is welcome in the Church of England".
The first flight taking seven asylum seekers to Rwanda was cancelled last week following a last-minute intervention by the European Court of Human Rights.
The legality of the policy will be tested in a court hearing in July.