Boko Haram, which means “western education is sinful”, has claimed responsibility for months of attacks in and around Maiduguri, the capital of Borno state. Strikes mainly target the police, churches and outdoor drinking areas.
More than 250 people have been killed since July 2010 by Boko Haram, rights groups say.
The seven-man committee, to be inaugurated on Tuesday, will be led by Borno civil servant Usman Gaji Galtimari. He headed a committee which produced a report following the 2009 Boko Haram uprising, in which hundreds of people were killed.
It will review all the security problems in the zone and make recommendations to bring a speedy end to the crisis, a government statement said.
Jonathan, who was sworn in for his first full term in office in late May, has previously voiced support for dialogue but the group has said it will only negotiate if its demands, including the resignation of the Borno state government, are met.
The committee was set up after a meeting between Jonathan and local Borno leaders, who have said the military has done more harm than good in reacting to attacks in the region.
Amnesty International has said brutalisation by security forces, unlawful arrests, killings and disappearances have been the operating practice in Maiduguri for months.
Thousands fled the city this month after clashes between security forces and Boko Haram intensified.
A further exodus began on Saturday after petrol station workers went on strike following the relocation of a fuel depot, thought to be too vulnerable in Maiduguri.
Bomb blasts in the north have replaced militant attacks on oil facilities hundreds of kilometres (miles) away in the southern Niger Delta as the main security threat in Nigeria.
Boko Haram strikes have spread farther afield in recent months, including a bomb in the car park of national police headquarters in the capital Abuja last month.
The group’s views, which include wanting sharia law more widely applied across Nigeria, are not backed by most of the country’s Muslim population, the largest in sub-Saharan Africa.
Borno state lies in the remote northeast, bordering Cameroon, Niger and Chad, and is one of the poorest regions in Nigeria