Transitional president Dioncounda Traore warns of “total war” against Tuareg fighters as he takes over from coup leader.

Mali’s interim president has been sworn in as part of a transitional plan to restore civilian rule following a military coup last month that has pitched the West African country into political chaos in the midst of a separatist rebellion.

Dioncounda Traore, 70, the speaker of the parliament, assumed office on Thursday in a ceremony in the capital Bamako attended by coup leader Captain Amadou Sanogo and other army officers.

The new leader faces the challenge of asserting control over northern parts of the country that are now controlled by Tuareg separatists, who have declared independence in the region they call Azawad, and other armed groups.

“I am president of a country that loves peace,” Traore said after the swearing-in. “I call on the rebels to halt all abuses.”

He said a peaceful route was the preferred option, but threatened all-out war if the separatists refused to agree to peace talks.

“We will not hesitate to wage a total and relentless war” unless the rebels left the cities they had occupied in the wake of the coup, Traore said, adding that he was prepared to negotiate with all groups apart from al-Qaeda.

Traore’s first task is to form a transitional government expected to comprise some 20 members, which he has said could include some of those who took part in the coup.

“This is definitely sending fresh hope for the return to civilian rule,” Al Jazeera’s Hashem Ahelbarra reported from the innauguration ceremony on Thursday.

Traore’s innauguration “will put an end to the political crisis which has been going on for the last few weeks here in the capital Bamako,” he said.

Traore is due to meet with key military and civilian officials this weekend to hammer out the details of the transitional period.

Under the agreement negotiated by the Economic Community Of West African States (ECOWAS) regional bloc, Traore has been tasked with organising elections to complete a return to democratic rule.

Transition under way

Al Jazeera’s Mohammed Vall reports from Timbuktu

“According to the deal he has 40 to 48 days to hold elections,” our correspondent said.

“But the vast territory in the north is now under the control of Islamist groups and Tuareg rebels so it makes it almost impossible at this particular moment to think about elections.

“So there is a debate about whether to go ahead with the elections within that time frame or wait for a military offensive in the northern part of the country and then set up proper elections.

“There is also the issue about whether the military leaders will quit and step aside or whether they will play a significant role in the transition period here in Mali,” Ahelbarra said.

Former president Amadou Toumani Toure was toppled by the coup on March 22. He formally resigned his position over the weekend, paving the way for Traore to take over.

Aid groups have warned of a humanitarian crisis and abuses against civilians in northern Mali, where more than 200,000 people have been displaced by fighting, drought and food shortages this year.

ECOWAS has also lifted its sanctions against land-locked Mali and agreed to give amnesty to all those involved in the coup as part of the transition deal.