"Nobody is saying that we would wipe off the Boko Haram before election is held in six weeks time, but we want to reconfigure the security architecture to make election conducive," Jonathan said in a media chat with journalists on Wednesday.
"I am sure that serious advances would be made in six weeks to make election conducive," he added.
Jonathan said that Boko Haram-held towns will be "liberated" in the next couple weeks.
"(Our army) is now better equipped," he said. "Our neighbors were not so committed before but that has changed now."
"With a better (military) platform and cooperative neighbors, people would know that we mean business in the next couple of weeks," he added.
The Nigerian leader went on to say that some 200 schoolgirls abducted by Boko Haram militants last year "be rescued and returned alive."
"As regards the Chibok girls, I don't want to be quoted as saying something but I'm sure the story of the Chibok girls will get better. We have put in place strategies and we are working with our neighbors. Just give us some time," he said.
Jonathan said that Nigeria's general election will be held.
"Elections would hold...and a new government would be sworn in by May 29 this year," he said, dismissing reports about a plot to sack the electoral commission chief.
"We will make sure that things are done in a way that nobody goes to war. We have a country (to protect). I'm not going to be president of another country, and so we cannot destroy the country," he said, in response to threats of violence by some of his supporters and loyalists of the opposition All Progressive Congress.
Nigeria has postponed general election until March 28 due to a deadly insurgency launched by Boko Haram in the northeastern region.