Police said bank manager Dipesh Shah was arrested at north-east Mumbai's Mulund on charges of transferring the money using the MobiKwik digital wallet.
"Shah has confessed that he transferred Rs 91 lakh from MobiKwik account to his private account at ICICI Bank via Mobikwik e-wallet," Cyber Crime Cell chief Anand Kumar Yadav told news agency IANS on Thursday. After appearing in a district court, Mr Shah was taken into police custody for six days.
In September, MobiKwik filed a police complaint in Gurgaon over the missing funds from the company's accounts. The case was then transferred to the Cyber Crime Cell.
MobiKwik offers a range of digital payments services and is available for use at more than 2.5 lakh online and offline points, the firm says on its website. It got the prepaid payment instrument licence from the Reserve Bank of India in July 2013.