Following the 2005 presidential elections, President Mahinda Rajapaksa appointed him as the Minister of State Banking Development in November 2005, but he resigned in April 2006 on a matter of policy.

Thereafter he was elected the Chairman of the Committee On Public Enterprises in July 2006 and presented the first report in January 2007, which led to serious controversies both local and overseas.

In 2017, he was sacked from his ministerial position by President Maithripala Sirisena at the request by the United National Party[5] due to his views against the privatisation and involvement of the judiciary by the government.

[6] Wijeyadasa Rajapakshe was appointed Minister of Justice, Prison Affairs and Constitutional Reforms by in May 2022 by Gotabaya Rajapaksa and continued in this capacity under Ranil Wickremesinghe.

[10] However on 20 May, the Colombo District Court issued an interim order preventing Rajapakshe from functioning as the party chairman, after considering a complaint submitted by Duminda Dissanayake.