In July 1999, while trying to engage in talks with the Russian side, Atgeriev was briefly arrested at Moscow's Vnukovo airport together with Chechen Deputy Prosecutor-General Adam Torkhashev and two officials from the Moscow office of the Chechen Interior Ministry. He has twice told Russian media that he alerted the then Federal Security Service of the Russian Federation (FSB) Director Vladimir Putin in the summer of 1999 to the imminent incursion into Dagestan. Atgeriev did not take active part in the Second Chechen War (at this time, he had no armed men under his command besides his personal bodyguards). Nevertheless, he was falsely implicated in the scandalous prisoner swap of Andrei Babitsky, a Russian journalist kidnapped by the Russian military.