The alleged theft by the Azizi Bank employee highlights the deep corruption in Afghanistan's banking sector, which already saw one leading institution unravel after revelations of massive fraud.
Investigators say at least 10 people aided the young woman, whom they identified only as Shogoofeh, in defrauding the bank.
Inayatullah Fazli, Azizi's chief executive, says the money was stolen two months ago.
Shogoofeh is alleged to have then used fake documents under the name Samira to reach India; her current whereabouts are unknown.