Law enforcement bodies detained Khaniyev, an Ingush resident, while investigating the 2004 Beslan school siege in North Ossetia.
"He gave evidence of his crime and the whereabouts of the Abu Dzeit camp that trained gunmen for the attack on Beslan," Shepel said.
Shepel said earlier that 90 gunmen involved in the attack had been identified as of late June, while 39 of them had been arrested, 19 killed and 33 placed on the wanted list. Eight gunmen were sentenced to long jail terms.
Gunmen raided the republic in the early hours of June 22, 2004, killing 78 people, including 35 police officers, and injuring 114 people, the Prosecutor General's Office reported.
Shepel said investigators had identified one of the attack's organizers, Kuwaiti national Abu Kuteip, who was close to Chechen warlord Shamil Basayev. He detonated a "martyr's belt" to avoid the arrest.
Shepel said 21 of the 31 gunmen killed in Beslan had been identified.
A group of 32 gunmen seized a school in the North Ossetian city of Beslan, North Caucasus, taking children and locals hostage on September 1, 2004. Troops stormed the school on September 3. The death toll in the attack hit 330, including 186 children, with 918 people rescued.
Thirty-one gunmen were killed. Nurpashi Kulayev, the survivor, is currently on trial for his role in the attack.