Senior Kogalymavia executive Alexander Smirnov said that "no technical failures" could account for why the Airbus 321 would have broken up in mid-air, as investigators have said happened.
"The only explanation is some kind of external action," Smirnov told a news conference in Moscow, without elaborating, adding that the doomed jet was in "excellent technical condition".
Both Cairo and Moscow have played down the claim from Egypt's IS branch that it brought down the aircraft flown by Kogalymavia between holiday destination Sharm el-Sheikh and Russia's second largest city on Saturday.
President Vladimir Putin described the crash as a "huge tragedy" in his first comments on the disaster at a meeting with the country's transport minister today, Russian news agencies reported.
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"Without any doubt everything must be done to create an objective picture of events so that we know what happened and can react accordingly," Putin said.
The Kremlin said the Russian president did not intend to speak to the nation or visit the relatives.
Russia has a dismal air safety record, and while larger carriers have begun upgrading ageing fleets, the crash is likely to raise concerns about smaller airlines such as Kogalymavia.
But Kogalymavia's executive Smirnov said the firm ruled out a technical fault or human error and said the plane had sustained "significant damage to its construction that did not allow it to continue the flight."
"The crew totally lost control and for that reason there was not one attempt to get in contact and report on the accident situation on board," Smirnov said.