The president gave the directive in his Democracy Day broadcast to the citizens of the West African country.
The Nigerian leader said the country's unity and stability as well as the protection of lives and property were non-negotiable, Xinhua reported.
He reaffirmed the determination of his administration to protect the nation's democracy, national unity and political stability, by waging a total war against terrorism.
The president said the activities of terror groups in the country had caused debilitating pains and horror on the nation, particularly the abduction of schoolgirls in Chibok, Borno.
"It is now 45 days since the horrifying abduction of the college girls of Chibok. I share the deep pain and anxiety of their parents and guardians," he added.
"I assure them once again that the government will continue to do everything possible to bring our daughters home," he said.
"I have also authorised the security forces to use any means necessary under the law to ensure that this is done," the president added.
The Islamist Boko Haram group has been the main source of terror in the country. The group is against Western education and wants to incorporate Sharia law in the country's constitution.
Last month, the group abducted over 200 college girls from Chibok.
According to Jonathan, the government would be open to dialogue and reconciliation with anyone or group willing to genuinely renounce terror.
The president underscored the need for all Nigerians to remain united to win the war against terrorism.
"The war against terror may be difficult, but the days of peace will come again. Terror is evil, nowhere in history has evil endured forever," he said.
The president commended the armed forces for the supreme price they had paid in confronting insecurity and urged Nigerians to always appreciate them rather than castigate them.
Jonathan expressed optimism that the nation would overcome its challenges and Nigeria would take its rightful place in the world.