Russia's emergencies ministry said the aircraft, a Boeing 737-800 operated by Dubai-based budget carrier Flydubai, crashed at 3:40 am (0040 GMT). Most of those on board were Russian.
"The aircraft hit the ground and broke into pieces," the Investigative Committee of Russia said in a statement on its website. "There were 55 passengers aboard and seven crew members. They all died."
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"Different versions of what happened are being looked into, including crew error, a technical failure and bad weather conditions," the committee said.
Flydubai's CEO Ghaith al-Ghaith told a press conference in the Gulf Arab emirate that it was "too early" to determine the cause of the crash.
"We will have information about the circumstances of the incident and the black box in the future, and an investigation is being conducted in cooperation with the Russian authorities and we are waiting to see the results," Ghaith said.
Dubai's civil aviation authority said it was sending an investigative team to Russia, president Ismail al Hosani said.
The plane was in a mid-air holding pattern for about two hours and the crash occurred more than two hours after the plane, flight number FZ981, was scheduled to land.
The plane came down inside the airport's perimeter, about 250 metres (yards) short of the start of the runway.
The plane's wing hit the ground on its second attempt to land and burst into flames, the Rostov region's emergency ministry said in a statement.
Grainy pictures from a security camera pointing towards the airport, which were broadcast on Russian television, showed a large explosion at ground level, with flames and sparks leaping high into the air.
According to the Flight Safety Foundation, there was strong wind with a speed of 12 metres per second, with gusts up to 19 metres, but visibility was reasonable.
Ghaith of Flydubai said that he had no information to indicate that the pilot had issued a distress call and said both the pilot and co-pilot, a Cypriot and a Spaniard respectively, each had over 5,000 hours of flight experience.
The crash is the budget airline's first since it started flying in May 2009. It last suffered a major safety incident when one of its planes was shot at while landing at Baghdad airport on January 27, 2015.
Six of the crew were non-Russians, the Russian emergency ministry said in a statement on it website, but it did not reveal the citizenship of the crew or passengers aboard.
Flydubai said in a statement that there were 44 Russians among the 55 passengers, eight Ukrainians, two Indians and one Uzbek. Four children were among the dead.
Russian President Vladimir Putin ordered for assistance to be given to the relatives of those killed. "The head of state said that now the main thing is to work with the families and the loved ones of those who had died," the Kremlin said in a statement on its website.
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