The Dubai-based airline's chief executive Ghaith al-Ghaith described such a suggestion as "speculation".
He told a news conference in Dubai that the Cypriot pilot and Spanish co-pilot each had nearly 6,000 hours of flying experience.
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The five other crew members were from Spain, Russia, the Seychelles, Colombia and Kyrgyzstan, he said.
"The aircraft was checked on Jan 21," Ghaith added.
The Boeing 737, which came from Dubai, was making its second attempt to land when it missed the runway in the southern Russian city of Rostov-on-Don, erupting in a fireball.
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Mr Ghaith said officials from the UAE civil aviation authorities and flydubai were going to Russia to participate in the investigation.
Asked if they would include explosive experts, civil aviation official Ismail al-Hosani told the same news conference: "No, there is nothing we said about (a) bomb."
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Cyprus President Nicos Anastasiades named the pilot as Aristos Socratous, expressing his "shock and deep sorrow" over the crash.
The Russian embassy in Nicosia said Mr Socratous was 38 years old and from the southern coastal town of Limassol.
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