All 92 people on board the Russian military Tu-154 died after it came down shortly after take-off near the resort town of Sochi.
Minister Maxim Sokolov said an “entire spectrum” of causes were being investigated, and added it was premature to speculate.
Viktor Ozerov, head of the Russian parliament’s defence committee, had earlier told state media that he “totally excludes” terrorism as a cause of the crash.
He said it could have been caused by a technical malfunction or crew error.
The plane was carrying 64 members of the renowned military choir and dance band, the Alexandrov Ensemble, including its conductor Valery Khalilov.
The ensemble, better known as the Red Army Choir, was heading to Syria to give a concert at a Russian air base.
Nine members of the media were among the 84 passengers on board. Eight crew were also on the plane.
Among the dead is Dr Yelizaveta Glinka, a renowned aid worker, who has been honoured by Russian President Vladimir Putin.
Mr Putin has ordered an investigation into the cause of the crash.
“I want to express my deepest condolences to families of our citizens who died,” he said.
“Tomorrow a nationwide mourning will be held in Russia.”
The Soviet-designed three-engine airliner disappeared minutes after taking off over the Black Sea.
The plane had departed at 5:40am local time (0240 GMT) from Adler, south of Sochi, where it had stopped to refuel after taking off from Moscow.
Several bodies have been recovered from the water. Some personal documents from those on board have also been found.
Fragments of the plane have been found about 1.5km (0.93 miles) from the Russian coast.
The plane was flying to Russia’s Hmeimim airbase outside the coastal Syrian city of Latakia, the ministry said.
More than 3,000 people – including divers – have been involved in the search operation, according to the defence ministry.
It said drones were being flown over the area to spot bodies and debris, and some 27 ships are involved in the operation.
The Tu-154 aircraft has been involved in a number of accidents in the past.
In April 2010 the-then Polish president Lech Kaczynski was killed when a Tu-154 airliner crashed near Smolensk in western Russia.