President Miguel Diaz-Canel said an investigation had been launched into the crash on Friday of the almost 40-year-old Boeing 737.
It was leased to the national carrier Cubana de Aviacion by a Mexican company.
Three women were pulled alive from the wreckage and are the only known survivors.
Details of some of the victims have emerged, including the Cuban Council of Churches saying that 20 priests from an evangelical church are among those who died in the crash.
Maite Quesada, a member of the council, said: “On that plane were 10 couples of pastors. Twenty people. All of the Nazarene Church in the eastern region.”
The group spent several days at a meeting in the capital and were returning to their homes and places of worship in the province of Holguin.
The Boeing 737 crashed a short time after taking off from Jose Marti airport and came down in a nearby field.
The period of mourning started from dawn on Saturday and will continue until to midnight on Sunday, the Communist Party leader and former president Raul Castro said.
The plane was on an internal flight from Havana to the eastern city of Holguin and was carrying mainly Cuban passengers, with five foreigners, including two Argentinians.
The plane, transporting a total of 104 passengers and six crew, was almost completely destroyed in the crash and fire that followed.
One of the wings of the plane was wedged among scorched tree trunks and the main fuselage was virtually destroyed.
Built in 1979, the aircraft was leased from a small Mexican company, Global Air, also known as Aerolineas Damoj.
Mexico is to send two civil aviation specialists to help in the investigation. The six crew members were Mexican nationals.
Boeing said in a statement that a “technical team stands ready to assist” and offered condolences to friends and relatives of the victims.
The 58-year-old Diaz-Canel, who succeeded Mr Castro as the communist island’s leader in April, appeared shocked as he watched the recovery operation.
Mr Castro sent his condolences to families bereaved in the “catastrophic accident”, while Russian President Vladimir Putin and various Latin American leaders also expressed sympathy.
Pope Francis asked the church in Cuba to convey condolences to families “who mourn the unexpected disappearance of loved ones”.
Jose Luis, 49, a supermarket worker near the airport, said he could see the plane taking off before it banked and plunged to the ground.
He said: “I saw it taking off. All of a sudden, it made a turn, and went down. We were all amazed.”
Yasniel Diaz, a 21-year-old musician, said the pilot appeared to attempt an emergency landing, but crashed instead.
He said: “The explosion shook everything. I started running, I was so afraid.”
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In Mexico City, anguished relatives and colleagues of the crew gathered outside the company’s offices demanding information.
Former Global Air employee, 44-year-old Ana Marlene Covarrubias, said: “I was friends with the captain, with the co-pilot, with the head flight attendant.
“When I heard the news on the phone, I thought it was one of those jokes people play.”