Ambassador Luca Attanasio, 43, and his bodyguard, Vittorio Iacovacci, 30, were killed while travelling from Goma, the country’s eastern regional capital, to visit a World Food Programme school feeding project in Rutshuru.
WFP driver Mustapha Milambo was also killed.
The two wooden coffins draped in Italian flags were loaded onto an Italian military cargo plane in Goma.
The plane then took off for Rome.
According to the country’s presidency, the two-car convoy had been stopped on the road north from Goma by six armed men, who killed driver Milambo and led the six other passengers away.
Army and park rangers tracked the group and a firefight ensued, during which the kidnappers shot the two Italians.
DR Congo’s interior ministry initially accused Hutu rebels from neighbouring Rwanda of the crime but the Democratic Forces of the Liberation of Rwanda (FDLR) denied any involvement in the attack.
The local governor said that the assailants spoke the Rwandan language Kinyarwanda.
The attack occurred in the territory of Nyiragongo, in North Kivu, an area where many rival rebel groups are based, according to local officials.
A specialised Carabinieri unit was expected to arrive on Tuesday in Kinshasha to help in an Italian investigation into the attack.
“The circumstances of this brutal attack are still unclear and no effort will be spared to shed light on what happened,” Foreign Minister Luigi Di Maio said.
More than 2000 civilians were killed last year in eastern DR Congo in violence by armed groups whose brutal attacks using machetes and heavy weapons have also displaced millions in what the UN calls one of the worst humanitarian crises as attacks ramp up.
DR Congo’s east is home to myriad rebel groups all vying for control of the mineral-rich land.