Rajapaksa has maintained that he is entitled to immunity as the complaint plainly accuses him of acts performed in his official capacity as the Secretary of Defense.
The case was filed by the International Organization of Truth and Justice Project on behalf of Ahimsa Wickrematunge, the daughter of late journalist Lasantha Wickrematunge.
She had lodged the case in July this year alleging Rajapksa for extra judicial killing, crimes against humanity and torture.
A spokesman for Gotabaya said that the case was totally politically motivated and there was no substance to back it up.
Gotabaya is mainly pitted against minister Sajith Premadasa at the elections scheduled for 16th of next month.