In 1995 he was appointed as Director-General, Department of Fiscal Policy and Economic Affairs in the Ministry of Finance and from 1997 to 1999 he served as the Deputy Secretary to the Treasury.
[2][4] In 2008, he was found guilty by the Supreme Court of Sri Lanka of a violation of procedure in the awarding of a large contract for the expansion of the Port of Colombo.
Jayasundera to once again take up the post of treasury secretary, he submitted a fundamental rights petition protesting the original decision to the Supreme Court, which was heard by the newly appointed Chief Judge who overturned the previous decision and allowed Jayasundera to be reinstated as secretary of the treasury.
[8] He along with former Treasury Secretary Attigala and former CBSL Governor Ajith Nivard Cabraal were later accused by Finance Minister Ali Sabry of preventing the Sri Lankan Government from approaching the IMF for a bailout in favor of a home grown solution which ultimately forced Sri Lanka into a preemptive sovereign default.
[9] Jayasundera along with the Rajapakasha brothers and others were found guilty of economic mismanagement between 2019 and 2022 by the Supreme Court of Sri Lanka which stated on 14 November 2023 that the respondents have breached the fundamental rights to equal protection of the law in terms of Article 12(1) of the Constitution in a fundamental rights petition filed by filed by Transparency International Sri Lanka (TISL) and other four activists.