Captain Mikhail Artamonov was ordered to be detained for 30 days under anti-terrorist legislation.
Investigators are studying what charges to bring against him, sources told the news agency.
Two men, an airline employee and a middleman - accused of helping two suspected Chechen female bombers to board two flights at Moscow's Domodedovo airport on 24 August in return for bribes - have already been arrested.
The women's passports were handed over to a police captain for verification, but the unidentified captain released them without carrying out any document checks or physical searches.
The planes went down on 24 August.
One was a Tupolev 154 with 46 people aboard a flight from Moscow to the Black Sea resort of Sochi, the other a Tupolev 134 with 44 people aboard, flying from the capital to Volgograd.
All 90 people on both planes were killed. Both planes left the same Moscow airport, Domodedovo, within about one hour of each other.
They went down at almost exactly the same time in different locations in southern and central Russia, hundreds of kilometres apart.