Akula will remain a consultant to the company until the end of March 2012 and assist with the transition, the company said in a press release.
There were no specific reasons as such given by the company. But the media reports say that he was facing trouble with the board members over management related issues.
Microfinance major also occurred losses worth Rs 384 crore during second quarter of FY12 against Rs 80.54 crore reported a year ago.
Akula started SKS Microfinance in 1997 and led the organization until 2004. He joined McKinsey & Company in Chicago as a management consultant, returned back to SKS in 2005 and turned the organization to a for-profit finance company.
SKS Microfinance is the only listed microfinance company in India. The company has provided over $5 billion in micro-credit to more than 7 million poor households across 22 states in India.
On Akula's resignation, PH Ravi Kumar, Interim Non-Executive Chairman of SKS Microfinance said, "The parting was amicable and the decision to step down is Mr Akula's. He is passionate about microfinance and SKS is no longer going to be only a microfinance company... We will be in the financial inclusion space."
Ravi Kumar is the former CEO of NCDEX, India's commodity exchange.