Jonathan said in an address marking 15 years since the return of civilian rule to Nigeria that no efforts would be spared to rescue the more than 200 girls kidnapped from a school in the northeastern town of Chibok in Borno state on April 14.
"I am determined to protect our democracy, our national unity and our political stability by waging a total war against terrorism," he said.
But on the same day as his vow to end the violence a military source and residents said Boko Haram had killed 35 people in separate attacks on three villages near the border with Cameroon, opening fire on villagers and torching homes.
"Boko Haram attacked the three villages yesterday morning in which 35 people were killed," a military officer in the Borno state capital Maiduguri told AFP on condition of anonymity.
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"The insurgents hurled petrol bombs into homes, setting them ablaze and shot residents as they tried to escape," he said.
The daring abduction of the teenage girls which sparked global outrage has drawn unprecedented attention to Boko Haram's extremist uprising with several foreign countries like the United States, Britain, France and China offering military aid and intelligence.
"I have instructed our security forces to launch a full-scale operation to put an end to the impunity of terrorists on our soil," Jonathan said.
Jonathan linked the Boko Haram group with foreign organisations such as Al Qaeda.