In May 2004 Dr. Wijeyadasa Rajapakshe was appointed as a Member of Parliament to represent the ruling Party, Sri Lanka Freedom Party and was offered the Ministry of Constitutional Affairs which was refused by him. Later he continued as the only Member of Parliament on the government side, without holding any portfolio.
After the Election of the Former President Mahinda Rajapaksa, he was sworn in as the Minister of State Banking Development in November 2005, but resigned in April 2006 on a matter of policy. He also resigned from the Organizer post of the Maharagama electorate.
Then he was elected the Chairman of COPE in July 2006 and presented the first report in January 2007, which led to serious controversies both local and overseas. He was recognized as a crusader who fought against corruption in the public sector, regardless of stature and the might of the politicians and the officials involved in such corruption.
His dedication to combat corruption and establish good governance was highly recognized by all patriotic segments in the country, and he was bestowed with the most prestigious award titled Sri Lankan of the year 2007 by LMD media services.