Boko Haram did not participate, he added, but the boys were abducted by bandits posing as the Islamist terrorist group.
CNN has not been able to verify this independently.
Some of the abducted children had addressed the Nigerian government in a video posted earlier on Thursday, bearing the Boko Haram logo.
In the video, a guy in a white shirt looks like someone off camera has helped him make the claims on behalf of the captors. He calls on the Nigerian government to close schools teaching “Western education” and says government troops sent to find the boys should withdraw.
The video shows dozens of children under a tree looking tired. The voice of the video claims to be Abubakar Shekau, leader of one of the Boko Haram factions.
Masari confirmed to CNN on Thursday that the children in the video are some of the abducted students. However, he discussed the voice claiming to be Shekau and said the “local bandits” were “imitating” his speech.
Speaking to CNN’s Becky Anderson on Wednesday, Masari did not completely dismiss the message, but warned that “more concrete evidence” was needed before confirming Boko Haram’s involvement.
Although kidnappings by rescuers by criminal elements in Katsina state have experienced a disturbing increase, a kidnapping of this scale is unprecedented. He recalls the brutal kidnapping of 276 Chibok girls in 2014 by the Shekau faction. More than 100 of these girls never returned home.
In 2018, a Boko Haram separatist faction known as ISWAP kidnapped more than 100 girls in Dapchi. All but one were released weeks later, after negotiations.
Obiageli Ezekwesili, co-founder of the #BringBackOurGirls movement and former Minister of Education in Nigeria, said she was “surprised” that the government had allowed another such kidnapping to take place.
CNN’s Stephanie Busari and David McKenzie contributed to this report.