Buhari announced the move in his inaugural speech on May 29, saying the Islamist insurgents would not be defeated until military command and control was transferred to the city at the heart of the uprising.
"A reconnaissance and advance team for the establishment of Military Command and Control Centre (MCCC) for OPERATION ZAMAN LAFIYA for the fight against terrorism and insurgency has moved to Maiduguri," an army statement said.
Army spokesman Sani Usman said the advance team was working to set up a fully functioning "forward command base" to coordinate the offensive against the Islamist rebels, who are blamed for more than 15,000 deaths since 2009.
"From now on, the fight against terrorism and insurgency would be monitored, coordinated and controlled from this centre," he added.
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Boko Haram was founded in Maiduguri, Borno state's capital, more than a decade ago and the group has carried out scores of attacks there over the last six years.
Addressing the conflict after he was sworn in, Buhari said "victory can not be achieved by basing the Command and Control Centre in Abuja...
Usman said another command centre was being set up in Yola, the capital of neighbouring Adamawa state, where two suicide bombers attacked a market last week, killing at least 31 people.
Yola had largely been spared from Islamist violence for the past several years.
At least 93 people have been killed in 11 suspected Boko Haram attacks since Buhari took office, highlighting the grave threat the group poses, despite recent gains by a four-nation offensive against the insurgents.
The offensive has liberated large swathes of territory from Boko Haram control but there are signs of the insurgents regrouping, especially in remote border regions.