Earlier the country's military said that Nigerian soldiers had thwarted a Boko Haram attack on Wednesday in the town of Biu in the restive northeastern section of the country.
Critics have accused Jonathan's government of not doing enough to address the insurgency, which mostly affects opposition strongholds.
Nigeria is holding presidential elections in February. Earlier this month, Jonathan launched his re-election bid in a raucous rally in Lagos.
The Nigerian Defense Headquarters said five terrorists and two anti-aircraft guns had been captured.
Officials gave no casualty tolls, but residents told CNN that at least 40 Boko Haram fighters were killed when they were surprised by Nigerian soldiers and fought a lengthy gun battle.
Scores of Boko Haram militants in 10 pickups and two motorcycles attempted to storm the town, 200 kilometers (about 124 miles) south of the Borno State capital, Maiduguri, around 7:30 a.m. local time. They were intercepted by soldiers from nearby military barracks, leading to two-hour gunfight, residents said.
Dozens of troops lay in wait for the militants and opened fire on an advance team of three pickups carrying the gunmen near an airstrip 2 kilometers (1.25 miles) outside Biu, residents said.
"Soldiers killed 40 Boko Haram insurgents and foiled their attempt to take over the barracks and attack the town," said Biu resident Mahmud Bukar. "All 30 gunmen in the three vehicles were killed by the barrage of gunfire from the soldiers."
The remaining gunmen who had camped at a gas station in nearby Kigir village mobilized and faced the troops in a fierce battle that lasted two hours, said Bashir Babagoni, another resident.
The gunmen were overwhelmed and forced to retreat in disarray, according to witnesses.
Soldiers, aided by local vigilantes, went on their trail in the bush while youths armed with crude weapons set up barricades in different parts of the town to prevent infiltration by the gunmen.
This was town's first attack
Residents trooped to the scene of the fighting to see the dead gunmen and their bullet-riddled vans, Babagoni said.
Biu is a religiously mixed town and the largest in southern Borno. It is an important commercial center that includes a large military base.
Although Boko Haram has carried out several raids on villages in the area in the past two years, Biu has never been attacked, residents said.
Boko Haram has terrorized northern Nigeria regularly since 2009, attacking police, schools, churches and civilians, and bombing government buildings. The Islamist group has said its aim is to impose a stricter form of Sharia law across Nigeria, which is split between a majority Muslim north and a mostly Christian south.
Last week, it brutalized a town and some villages near the border with Chad, killing hundreds, perhaps thousands of people. Human Rights Watch said it acquired satellite imagery
that shows the results of fires set by Boko Haram. The rights group said 11% of Baga and 57% of Doro Gowan were scarred by the flames.
Tactics have horrified the world
Boko Haram's brutal tactics have shocked and stunned the world.
It has kidnapped students, including more than 200 schoolgirls who were abducted in April and remain missing.
It has also strapped bombs to young girls and ordered them to blow themselves up in markets, according to one teenager who said she refused and fled the scene of an attack.