Governor Kashim Shettima travelled to the capital Abuja for talks with Jonathan and Nigeria's security chiefs following the latest massacre in Borno of 106 people in the mostly Christian village of Izghe on Saturday. (Agencies)
"We are in a state of war. That is what I came to tell the president," Shettima told reporters after the meeting.
"I made it emphatically clear to Mr. President that Boko Haram are better armed and better motivated," than the security forces, he added.
Unless more troops and more resources are deployed to Borno, "it is absolutely impossible for us to defeat Boko Haram," the Governor said.
Borno along with two neighbouring northeastern states was placed under emergency rule in May, when the military launched a major offensive aimed at crushing the Islamist uprising which has killed thousands since 2009.
Attacks have continued despite the beefed up military presence. Borno, where Boko Haram was founded in 2002, has been the hardest hit area.
The extremist militia has said it is fighting to create a strict Islamic state in the country's mainly Muslim north.
Shettima said the Islamists have been able to attack defenceless civilians with ease and made reference to a slaughter last week in the town of Konduga where gunmen seemingly killed residents at-will "for over five hours".
"Have we ever succeeded in thwarting any of their plans?" the governor further said. He provided a death toll of 106 for the Izghe attack, supporting figures given by other area officials.
"Some were hospitalized with very great injuries, so I am afraid the figures might climb," he said.
The attackers reportedly went door-to-door looking for residents who were hiding, undeterred by the security forces. Those who were found were dragged outside, gathered together and slaughtered, witnesses said.
While Jonathan has at times sought to portray the military offensive as a success, outrage in the region is building following the repeated failure of the security forces to prevent major attacks, including some in the heart of Borno's capital Maiduguri.
Governor Kashim Shettima travelled to the capital Abuja for talks with Jonathan and Nigeria's security chiefs following the latest massacre in Borno of 106 people in the mostly Christian village of Izghe on Saturday.