Lt. Gen. Shavendra Silva, who became army commander last week, faces allegations of grave rights abuses during the war, which ended in 2009 after government forces defeated ethnic Tamil rebels who fought to create a separate state.
"I, of course, totally deny those allegations," Silva told reporters at his first media briefing since his appointment. "Those are allegations. Anyone can make any allegations."
The U.N. human rights chief, the United States and the European Union expressed concern last week about Silva's selection, saying it undermines the post-war justice and reconciliation process which the government has promised to undertake.
Silva was in charge of the 58th Division, one of the groups that encircled the final stronghold of the Tamil Tiger rebels in the last stages of the war.
According to a 2015 investigation by the U.N. office of the High Commissioner for Human Rights, near the end of the war Silva was tasked with capturing the Putumattalan area from the Tamil Tigers. It found evidence that both a hospital and a U.N. hub were shelled.
The investigation cited witnesses as saying cluster-type munitions were used by the Sri Lankan armed forces in their attacks on Putumattalan hospital and the United Nations hub. The government promised the U.N. Human Rights Council in 2015 that it would investigate the allegations and involve foreign prosecutors and judges, but nothing has been done so far.
Both the Sri Lankan military and the rebels have been accused of wartime abuses. The United Nations has said some 45,000 Tamil civilians may have been killed in the final months of the conflict.
U.N. High Commissioner for Human Rights Michelle Bachelet said last week that Silva's appointment could impact Sri Lanka's ability to contribute to U.N. peacekeeping missions.
In Washington, a senior State Department official said last week that the United States was "deeply concerned" by Silva's appointment and was registering its objections. The official, who was not authorized to discuss diplomatic discussions publicly and spoke to reporters on condition of anonymity, said the appointment could affect cooperation and improved military relations between Washington and Colombo.
The official also said the appointment "undermines Sri Lanka's international reputation and its commitments to promote justice and accountability." The official added that should Silva remain in the post it might also hurt a planned $480 million Millennium Challenge Corporation grant intended to help the country modernize its urban transport system and networks.