Channel 4 said two Sri Lankan soldiers who declined to be named had told them that orders to execute surrendering rebels came directly from the defence secretary, who is the younger brother of President Mahinda Rajapakse.
"One of these eyewitnesses, an army officer, accuses defence secretary Gotabaya Rajapakse of ordering Brigadier Shavendra Silva to execute Tamil rebel leaders," the report said.
Sri Lanka's then army chief, Sarath Fonseka, has been charged with inciting violence and causing racial hatred for allegedly making a similar statement implicating Rajapakse, who has vehemently denied ordering any executions.
"This (latest Channel 4 report) is completely false," Medawela told AFP. "None of the things described by Channel 4 has taken place. This latest report is aimed at strengthening their previous claims."Channel 4 said Rajapakse himself denied the allegation.
The channel quoted a soldier as saying that the defence secretary had wanted troops "to finish the job by whatever means necessary".
"He said this was interpreted by the soldiers as a licence to kill," the broadcast said.
The UN has said there are "credible allegations" of war crimes and noted that tens of thousands of civilians perished in the final stage of the fighting in Sri Lanka.
The government in Colombo has consistently denied any war crimes happened while it crushed the Tigers, ending decades of ethnic conflict, and has also resisted calls for an international probe.
Sri Lanka's former president, Chandrika Kumaratunga, on Sunday broke ranks with her ruling party and expressed shock over last month's Channel 4 documentary, titled Sri Lanka's Killing Fields.
Sri Lankan authorities have rejected the documentary, which showed alleged executions by government troops, as fake.
The programme has been shown in many countries, including the US, Australia and India, where there are considerable Tamil communities.