An international arrest warrant has been issued for her and at least nine other accomplices. The revelations are another embarrassment for the banking sector in the country, which has seen corruption unravel one major institution amid ongoing security threats from militants and criminals.
Shokofa Salehi, 22, worked in the money transfer division at the headquarters of Azizi Bank, a major lender in Kabul. She disappeared around two months ago, chief executive Inayatullah Fazli said, suspected of transferring $1.1m (£700,000) out of the bank's coffers to accounts of relatives.
It is thought she used fake documents under the name Samira to reach India after transferring the money and her current whereabouts are unknown.
Two suspects in the case have been detained in Dubai and police are also looking for Ms Salehi's parents who are believed to have returned to Kabul after going with her to India.
Azizi Bank opened in 2006 and says it has "a 1500-plus strong team of employees and with a 20% female work force is playing a quiet but effective role in women('s) emancipation and empowerment". It also calls itself "the bank you can trust".
Ms Salehi's alleged pilfering pales in comparison to some other examples of corruption in Afghanistan's banking sector.
In 2010, regulators seized Kabul Bank, Afghanistan's largest lender, amid allegations of severe levels of corruption. Its near-collapse and subsequent bailout represented more than 5% of Afghanistan's gross domestic product, making it one of the largest banking failures in the world in relative terms.
Earlier this year, two top Kabul Bank executives were jailed for five years for stealing funds. Critics said the punishments were far too light and raised questions about President Hamid Karzai's commitment to rooting out corruption.
Banks in Afghanistan have also been targeted by Taliban militants and criminal gangs.