In a letter sent to the Archbishop of Glasgow, the Apostolic Nuncio Archbishop Antonio Mennini outlined the Pope's sympathies.
He said: "Having learned the sad news of the tragic accident which occurred in Glasgow when a police helicopter crashed into Clutha Vaults pub, close to the Cathedral, causing the death of several people and numerous injured, I would like hereby to convey to you, as Archbishop of Glasgow, the closeness of the Holy Father as well as my most sincere sympathy in these difficult moments.
"I assure you of my prayers for those who have tragically lost their lives or have been injured as well as their relatives. "May the Lord grant eternal rest to those who have died and comfort their relatives and the entire community of Glasgow in these moments of distress and sadness."
Meanwhile, Christians are being encouraged to keep praying for all those involved in Friday's helicopter crash in Glasgow. Fire crews are today doing a final search to make sure no one else is inside after the remains of the aircraft was removed earlier on. Nine people are confirmed dead after the helicopter came down on the Clutha at 10:25pm on Friday evening.
Three who died were on board while the other six were inside the pub. Today it was confirmed the helicopter sent no distress signal and came down intact. The remains are now being taken to the Air Accident Investigation Branch's headquarters in Hampshire to be examined.
Over the weekend churches across the city stopped to pray for all those caught up in the incident.
The Catholic Archbishop of Glasgow Philip Tartaglia led prayers at St Andrews Cathedral for the victims - and others: "Those who are bereaved and all the rescuers both the emergency services and members of the public. "And we pray for our city of Glasgow."
Revd Dr Laurence Whitley from Glasgow Cathedral is warning that the shock of the weekend will now turn to grief and is calling on believers to remember victims, families of victims and emergency services in prayer. Speaking to Premier's Marcus Jones on the News Hour - from the scene - he explained how local people are coping.
Families of those still missing following the incident on Friday have expressed anger at the slow pace of the recovery operation. But Fire Service Chaplain, Revd Gordon Armstrong has been defending the emergency services claiming they're doing all they can.
He said: "I have to say I'm very proud of the way all the emergency services are pulling together and working together. It is not a nice situation to be in and there's that frustration that we all want this to be resolved and resolved as soon as possible.
"They are a remarkable group of people and working to the best of their ability."
Friday's incident will be marked in the House of Lords this afternoon. Rt Revd Dr Alastair Redfern is the Bishop of Derby and will be in the House. He tells Premier he's been pleased to hear of the impact local chaplains have been having on all those affected by the incident.
Twelve people injured on Friday are said to be still in Hospital. Meanwhile a book of condolence has also been opened at Glasgow City Chambers.