The militant group last week claimed responsibility for yet another church attack which killed six in Potiskum, north-eastern Nigeria.
Boko Haram is thought to be responsible for more than 10,000 deaths since 2009.
President Muhammadu Buhari has appointed a number of new defence chiefs following the removal of the heads of the army, navy and air force.
Maj Gen Tukur Yusuf Buratai, who will look after the Army, and National Security Adviser Maj Gen Babagana Monguno, both come from Borno State - the centre of fighting.
A statement, released by the Nigerian government on behalf of the president said: "Nigerians are a very religious people and President Buhari believes that the terrorists who wantonly attack our places of worship have willfully declared war on all that we value, and must therefore be confronted with all our might and collective resolve.
"The President reaffirms his administration's total commitment to doing everything possible to eradicate Boko Haram, terrorism and mindless extremism from Nigeria in the shortest possible time.
"President Buhari assures all Nigerians that terrorism will ultimately be defeated and full security restored in all parts of the country for people to safely practice their respective faiths with liberty wherever they may reside in the nation."
The outgoing army chief, Lt Gen Kenneth Minimah, had recently said the isolated attacks were a result of how strong the army had become. He claimed terrorists were resorting to cowardly tactics by targeting civilians.