Three people on board the helicopter died when it landed on the Clutha Vaults in Glasgow as it returned from a police operation on Friday night. Six people inside the pub were killed.
The wreckage of the three-tonne Eurocopter has been removed in a painstaking operation which allowed emergency services to begin searching the area inside the bar.
An investigation into what caused the helicopter to drop out of the sky "like a stone" is under way.
Pilot David Traill, 51, died along with police officers Kirsty Nelis, 36, and Tony Collins, 43.
Two victims who were inside the pub have been named as 48-year-old Gary Arthur, from Paisley, and Samuel McGhee, 56, from Glasgow.
Two private ambulances, escorted by Police Scotland outriders, left the scene of the tragedy an hour after the fuselage was winched out of the roof.
Firefighters, ambulance staff and police officers formed a guard of honour and saluted as the vehicles passed by.
Police Scotland's Deputy Chief Constable, Rose Fitzpatrick, said: "The body of the ninth person has now been removed from the scene and taken to the Southern General Hospital for formal identification.
"In due course the wreckage of the helicopter will be removed and will be taken for detailed examination and investigation by the Air Accidents Investigation Branch Farnborough facility.
"This now enables us, working with colleagues from the Scottish Fire and Rescue Service, to continue the search and recovery operation within the site to satisfy ourselves that all the victims of Friday night's tragic incident have been recovered.
"This continues to be a difficult and complex operation. A painstaking process is under way to search and also to preserve the scene which is, of course, subject to investigation.
"The uncertainty for the families of those who have died is at the front of our minds. It remains our absolute priority to give clarity to those affected as soon as we are able.
"The loss of so many people has been deeply felt."
The popular bar was packed with more than 100 people when the accident happened at 10.25pm.
A total of 32 people were taken to hospitals across the city.
NHS Greater Glasgow and Clyde said 12 remain in hospital. Eight are being treated at Glasgow Royal Infirmary and one at the Western Infirmary. Two patients have been transferred to the National Queen Elizabeth Spinal Injuries Unit at Southern General Hospital, taking the total number of patients at that unit to three.
Scottish Fire and Rescue Service assistant chief officer David Goodhew said the construction of the Clutha had hampered the "extremely difficult and complex" recovery operation.
He said rescuers had to contend with large amounts of rubble inside the building, caused by the collapse of three roof structures and walls inside the pub.
Mr Goodhew said: "We have recovered nine bodies so far. They have been removed and we are now doing a further search. It's anticipated that search will be concluded within the next few hours, just to ensure that there is nobody else in there at all.
"Of course we are hoping that there is no one else in there but before we actually confirm it we need to be doubly, doubly sure that there's nobody in there."
There has been some criticism over the speed of the rescue operation from the families of those still missing.
Mark O'Prey has not been seen since the aircraft came down and relatives said they believed the helicopter recovery was taking precedence over the removal of bodies.
His sister Louise told BBC Radio Scotland's Good Morning Scotland programme: "We just need to know. It's too long now, really.
"We feel as a family that the priority is given to the integrity and keeping that helicopter intact, which is no use to us."
John McGarrigle said his father John Snr was in the Clutha and has not yet been found.
Speaking at the crash site, he said: "I just want the phone call we were told we were going to get from the police.
"I know he was in there, there's eyewitness accounts from people in there. My dad's been a local in there for years."
Scotland's Deputy First Minister Nicola Sturgeon said crews had been working as quickly and safely as possible but that she understood the "frustration and the anguish" of people who are waiting for news.
Ms Sturgeon visited Scottish Ambulance Service staff in Springburn, Glasgow, to thank them for their response to the crash.
She said: "We've seen significant progress at the site today with the lifting of the helicopter. In light of that, it is appropriate again to say how much all of us are thinking of those who have been bereaved.
"It is not possible to imagine the grief and the anguish that they are suffering but I hope it is of comfort to them that they know that the thoughts not just of the people across Glasgow but people across the country are with them.
"There are also people still in hospital suffering from injuries and our thoughts and good wishes are with all of them as well."
The first ambulance was on scene within one minute of a call to the emergency services and was quickly supported by another 10 crews, the ambulance service said.
Gary Hardacre, head of risk and resilience, said: "We would like to pass out heartfelt condolences to all of those who have been affected by the incident."
The helicopter, covered by a tarpaulin, was put on to a low loader lorry and driven away.
The teenage daughter of Paisley victim Gary Arthur, 48, is a Celtic and Scottish women's footballer.
Today Celtic manager Neil Lennon added a wreath to the hundreds of floral tributes placed at the site of the crash.
"It's an unforseen tragedy that's affected the whole city, and the city is united in grief at the minute. There's an eerie atmosphere around the place at the minute, which you can understand," he said.
"I was out myself on Friday night with some friends when I heard, so it puts a lot of things in perspective.
"Our own club has been affected indirectly with a young girl who plays with the ladies' team losing her father, so I just wanted to come down on behalf of the club and pay respects to all the people involved.
"It's very difficult for me to find the right words at this time for (the victims and families) but, on behalf of myself and the club and the Celtic support, we're all thinking of you and you're very much in our thoughts and prayers at this time."
Chloe Arthur, 18, said following her father's death: "I promise to do you proud."
She wrote on Twitter: ''RIP dad. You'll always mean the world to me. I love you with all my heart."