Dioncounda Traore, who was sworn in Thursday, took over 22 days after a military coup ended more than 20 years of democratic rule in the West African country, The New York Times reported.
"Mali has never experienced such difficult times," Traore said after being sworn in. "Its very existence as a nation is at stake."
Traore, a 70-year-old labor union activist who had been the leader of the country's National Assembly, said he hopes the rebels, who have proclaimed their own country, Azawad, and the Islamic group Ansar Dine will leave peacefully, Voice of America reported.
If necessary, Traore said: "We will not hesitate to mount a total and relentless war to recover our territorial integrity, but also to kick out al-Qaida and drug traffickers who have been operating in the north for years, as well as hostage-takers that discredit our country and impede our development."
In northern Mali, measures must be taken to ensure the safety of civilians, said the U.N. commissioner for human rights, Navi Pillay.
"Reports from the north of the country suggest that civilians have been killed, robbed, raped and forced to flee," Pillay said. "It is difficult at this point to be sure of the scale of the human rights violations taking place, but in addition to preying on individuals, a variety of different rebel groups have been accused of looting private and public property, including hospitals and healthcare facilities."
The north has been beset by looting and food and water is in short supply, VOA said.