Rajapakse, who is a President's Counsel, also resigned as organizer for the Maharagama electorate of the Sri Lanka Freedom Party of President Mahinda Rajapakse.
Both hail from the President's hometown in the southern Hambantota district.
Rajapakse was appointed deputy foreign minister by President Rajapakse soon after coming to office, but he refused to take up the appointment.
The President later created the Ministry of State Banks & Development and he was made full Minister, without cabinet ranking.
However, former Minister Rajapakse had told confidantes that he was unhappy over the difficulty in implementing his ideas and also did not have specific staff or a secretary.
He also pushed the plan to revive the failed Pramuka Bank with state support.
Rajapakse was also trying to bring changes to the acts governing the State Mortgage and Investment Banka and the National Savings Bank.