Charges against Sajin de Vass Gunawardena in the Colombo Chief Magistrate's Court have been filed under the Declaration of Assets and Liabilities Law, the Commission to Investigate Allegations of Bribery or Corruption said.
Gunawardena, who served as Rajapksa's foreign policy advisor, is a current member of parliament.
He was overlooking the Foreign Ministry for Rajapaksa in its day-to-day running.
The Bribery Commission has questioned both Gunawardena and his wife over accusations that his assets exceeded his income.
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He was questioned over the loss to the government as a result of an executive decision made by him outside cabinet approval.
Since Rajapaksa's defeat in the presidential election in January, the former President's family members have been reported to the anti-graft panel.
Yesterday, the government announced that it had traced more than a billion dollars in public funds allegedly stolen by members of the former regime.