The article in La Civiltà Cattolica, which reportedly was backed by the Vatican, speaks of an alliance of hate.
It reads: "The most dangerous prospect for this strange ecumenism is attributable to its xenophobic and Islamophobic vision that wants walls and purifying deportations.
"The word 'ecumenism' transforms into a paradox, into an 'ecumenism of hate'."
In a letter of response, seen by Premier, Rev Johnnie Moore (pictured) - an advisor to President Trump says a conversation between the parties is "urgent".
He writes: "It's in this moment of ongoing persecution, political division and global conflict that we have also witnessed efforts to divide Catholics and Evangelicals.
"We think it would be of great benefit to sit together and to discuss these things.
"Then, when we disagree we can do it within the context of friendship. Though, I'm sure we will find once again that we agree far more than we disagree, and we can work together with diligence on those areas of agreement."
In the run up to the election, Pope Francis criticised President Trump's plans to build a wall on the border with Mexico labelling it un-Christian.
Since taking office Trump has since met the pontiff at the Vatican.