On Monday, suspected Boko Haram suicide bombers attacked a mosque and another location within the university.
The blasts killed four people and injured 17 others, as of first count.
In a audio recording published on YouTube, Shekau said the mosque was attacked because it was “ungodly”.
He reiterated that the Nigerian army did not kill any of his members in the Sambisa forest.
“The bomb that happened this morning, it’s my people. Don’t deceive people that it’s a mosque, how would you build a mosque and do ungodly things in it,” Shekau said in the recording.
“We are not angry with Nigeria. You didn’t kill anyone in Sambisa. We are praying that we don’t change; Koran is our teacher; this is the message we are sending to you. Are you [Buhari] as powerful as God?
“You should know it’s Shekau talking and I’m alive and it’s we that did it, even if King Pharaoh repents, we will not accept it.”