It asked for an international investigation into the massacre.
The report did not reveal any direct evidence but cited confidential conversations the group and other independent researchers had with witnesses.
The aid group, Red Cross and a Nordic mission monitoring a collapsing cease-fire at the time were denied access to Muttur town for days. Action Against Hunger added that police did not preserve the crime scene and evidence.
Police investigations and a subsequent presidential inquiry were also undertaken working on the premise that security forces were not involved in the killing and conducted in a way to hold the rebels, local Muslims and the aid group itself responsible, the report said.
Family and other witnesses were threatened to deter them from testifying against government forces and there was constant government interference in investigations, the report said.
Military spokesman Brig. Ruwan Wanigasooriya said the government "remains committed to conduct impartial and comprehensive criminal investigations and domestic inquiries into any complaints and information received, relating to alleged perpetration of crimes by members of the armed forces and the police."
The government earlier accused the rebels of killing the aid workers and said the aid group's headquarters had exposed them to danger.
Sri Lankan forces and the now defeated Tamil Tiger rebels, who fought for an independent state for ethnic minority Tamils, are accused of serious human rights violations and possible war crimes during the quarter-century civil war, which ended in 2009.
The country has so far ignored calls for a thorough local inquiry into war abuses and says it will not allow any international probe.