Vatican Radio reported that the Pope said this during an Oct. 10 private meeting with the Ark Community, which was founded by his late friend, Tony Palmer.
Palmer was recognized globally as a friend of the Pope when he facilitated the recording of a papal message sent to Kenneth Copeland Ministries in February.
Palmer died suddenly in July when he was in a traffic accident.
Vatican Radio reported that Pope Francis thanked Palmer’s widow and the new leader of the community, Archbishop Robert Wise, for carrying forward the dream of walking together in communion. 
“We are sinning against Christ’s will” the Pope said, “because we continue to focus on our differences,” but “our shared baptism is more important than our differences.”
While the devil, the “father of lies” divides us, the Pope added, we are called to preach the Gospel in every corner of the earth, with the certainty that He is with us. “We each have in our churches excellent theologians,” the Pope said, “but we shouldn’t wait for them to reach agreement.”
The Holy Father noted that denomination does not matter for Christians who are suffering the same persecution in places such as the Middle East or regions of Africa.
A video of the informal meeting and the Pope's off-the-cuff comments, recorded by a member of the Community, is here: https://www.youtube.com/watch?v=k-8ahwAT5_k (The Pope speaks in Spanish and a priest translates his comments to English.)