An army spokesman said jets and helicopter gunships had been used to attack several camps.
He told the BBC that a plane had been hit by anti-aircraft fire but had managed to return to base.
States of emergency were declared this week in three north-eastern states hit by Boko Haram’s Islamist insurgency.
Nigerian military spokesman Brig Gen Chris Olukolade said two militant bases in the Sambisa Forest Reserve were destroyed in raids.
The reserve is about 70km (45 miles) south of the Borno state capital, Maiduguri, where the militants first emerged in 2009.
Reports say dozens of militants have been killed, but there has been no independent confirmation.
Nigerian forces are trying to regain control in the states of Adamawa, Yobe and Borno.
“It is not just Sambisa, every camp is under attack,” the Reuters news agency quoted Brig Gen Olukolade as saying.