Mahesh Murthy, 52, is the co-founder of Seedfund and the founder and chief executive officer of Pinstorm Technologies Private Limited, a pay-for-performance digital brand management firm.
As per the complainant in the new case, Mr Murthy allegedly sexually harassed her about 14 years ago, a senior police official said.
The woman approached the Bandra police in connection with the matter on March 19, following which an FIR was registered, he said.
"Based on the woman's statement, we have registered a case under Indian Penal Code sections 354 (sexual harassment) and 509 (word, gesture or act intended to outrage a woman's modesty) against Murthy," the official said.
As per the woman, Mr Murthy allegedly touched her inappropriately during a meeting at a coffee shop in suburban Bandra in 2004, the official said.
Last month, the police in suburban Khar had arrested Murthy in connection with a molestation case, based on a complaint filed by a Delhi-based woman entrepreneur.
The case was registered by the Khar police here as the complainant mentioned that Murthy was a resident of Mumbai.
The National Commission for Women had written to the Maharashtra Police about complaints it had received from several women against the angel investor, a police official said.
Last year, a business author had alleged that she was sexually assaulted by Murthy, a claim rubbished by him.
In April last year, a series of complaints surfaced on social media against Mr Murthy. These included some charges dating back a decade ago, the police had said.