41-year-old Asher Samson had been in a lengthy legal battle to stay in the UK since he arrived in 2004 after suffering persecution.
He claimed he had been beaten and threatened with execution by Islamic extremists in Pakistan.
Premier was able to speak to Mr Samson earlier this month as he waited to be transported to a detention centre. However the leader of the church he attended before his removal confirmed that his application to remain had been denied.
Rev Lorraine Shorton from Hall Green United Community Church said on Premier's News Hour: "I've received some messages from him. He's very scared, he's fearful for his life.
"He's in hiding in Pakistan and his family are terribly worried for him."
This comes as new research from the Catholic Church has found that 187 Christians are facing blasphemy charges in Pakistan.
Rev Lorraine said it was essential that Asher's case be reopened.
Sharing her message to the Home Office, she said: "I would ask them to look again and bring Asher home to where he is safe.
"Jeremy Hunt on the 18th January - just this week, was talking with the Open Doors UK charity and said, 'no one should face persecution for their faith where ever they are' and that includes Christians.
"But the UK is sending people back to these countries where their lives are in danger. Pakistan is number five on the World Watch List for extremism against Christians and it's just disgraceful really that we're sending people potentially to their death."
She also called for prayers for both Mr Asher and his family that are mostly in the UK.
"Just pray for Asher's safety - that is paramount. At the moment he has no funds to live on - he can't work.
"Pray for Asher's family that they can get the support and the legal help needed and just pray for the whole community because the whole community has been rocked by this latest event.
"Pray that the government will see sense."
Premier has previously contacted the Home Office for a comment.
Listen to Premier's Eno Adeogun speaking with Rev Lorraine Shorton: