According to Voice of America, villagers of Shekau, the insurgent group leader's hometown in Yobe state, confirmed that Falmata Abubakar was the mother of Nigeria’s most wanted man.
Shekau's father was a local district imam before passing away a few years ago.
Falmata had never spoken to reporters before, and said she was praying to God to show her notorious son the good way.
She said her son left the village as a young man to study Islam in Maiduguri - the epicentre of the group's insurgency - where he met Boko Haram's founding leader Muhammed Yusuf, who ensured that he did not return home.
"I don’t know if he's alive or dead. I don't know. It's only God who knows. For 15 years I haven't seen him. Since Shekau met with Mohammed Yusuf, I didn't see him again.” Falmata was quoted as saying.
She added: “Yes, he's my son and every mother loves her son, but we have different characters.”
"He brought a lot of problems to many people. Where can I meet him to tell him that these things he is doing are very bad? He brought many problems to many people, but I am praying for God to show him the good way."
Boko Haram is known as one of the most deadly active terrorist groups in the world, formed to fight against Nigeria's government in 2009 with the aim of establishing an Islamic caliphate in west Africa.
The group is mainly focused in north-eastern Nigeria, the Lake Chad region, and has reportedly left more than 20 000 people dead, with some two million displaced.
Boko Haram pledged allegiance to the Islamic State group (ISIS) in March 2015. In August 2016, the group apparently split, with an ISIS video announcing that Shekau had been replaced by Abu Musab al-Barnawi, the son of Boko Haram's founder.