Jonathan has removed his Defence Minister Bello Mohammed but his replacement is ye to be announced.
"The president has relieved the National Security Adviser of his job and replaced him with Colonel Sambo Dasuki. The president has also sacked the minister of defence and will announce his replacement later," presidential spokesman Reuben Abati said in a statement, released after a meeting held by the president with his top security chiefs following a new wave of terrorist attacks in some states in northern Nigeria.
On Sunday, suicide bombers of Islamic fundamentalist group Boko Haram went to three churches and killed around 18 persons in Nigeria's northern state of Kaduna triggering a reprisal that increased the death toll beyond 80.
Another attack in neighbouring state of Yobe by the insurgents on Monday brought the total death to 101.
Jonathan and his security chiefs have come under heightened criticism for improper handling of the insurgency by Boko Haram. Three suicide bombings at churches sparked repraisals from Christians who burnt mosques and killed dozens of Muslims.
Boko Haram has threatened to turn the oil rich African country into a Muslim caliphate.