Last week President Goodluck Jonathan asked a high level team to look into the possibility of granting the militants a pardon.
The announcement was made via an audio statement believed to be from the group's leader Abubakar Shekau.
In recent years Boko Haram has carried out a campaign of violence across northern and parts of central Nigeria killing at least 2,000 people.
Founded in 2002
Official Arabic name, Jama'atu Ahlis Sunna Lidda'awati wal-Jihad, means "People Committed to the Propagation of the Prophet's Teachings and Jihad"
Initially focused on opposing Western education
Nicknamed Boko Haram, a phrase in the local Hausa language meaning, "Western education is forbidden"
Launches military operations in 2009 to create an Islamic state across Nigeria. Founding leader Mohammed Yusuf killed in same year in police custody
Succeeded by Abubakar Shekau, who is said to be well-versed in theology. Suspected to have split into rival factions in 2012
The group says its members are fighting to create an Islamic state in Nigeria's predominantly Muslim north.
Mr Shekau said his group had done no wrong and so an amnesty would not be applicable to them.
It was the Nigerian government that was committing atrocities against Muslims, he said.
"Surprisingly, the Nigerian government is talking about granting us amnesty. What wrong have we done? On the contrary, it is we that should grant you [a] pardon," AFP news agency quotes him as saying in the Hausa language audio recording.
BBC Nigeria correspondent Will Ross says that northern religious and political leaders have been urging President Jonathan to grant an amnesty to the militants as they say the army's response to the insurgency is not bringing peace.
The amnesty panel was set up by the president last week and includes senior military representatives, presidential sources said.
The move surprised many as President Jonathan had dismissed the idea of amnesty and dialogue, our reporter says.
In 2009, then-Nigerian President Musa Yar Adua granted an amnesty to thousands of militants wreaking havoc in the oil-rich Niger Delta in the south.
The violence fell dramatically but there are worrying warnings of further unrest in the Delta, analysts say.