Boko Haram was not involved, he added, but the boys were previously kidnapped by bandits posing as the Islamist terror group.
CNN has not been able to independently verify this.
Some of the kidnapped children had addressed the Nigerian government in a video released earlier on Thursday that bore the Boko Haram logo.
In the video, a boy in a white shirt appears to have been persuaded by someone off camera to make the demands on behalf of the kidnappers. He asks the Nigerian government to close schools that provide “Western education” and says government forces sent to find the boys should withdraw.
The video shows dozens of children under a tree looking tired. The voice in the video claims to be Abubakar Shekau, a leader of one of Boko Haram’s factions.
Masari confirmed to CNN on Thursday that the children in the video are some of the kidnapped students. However, he disputed the voice claiming to be Shekau, saying instead that “local bandits” were “mimicking” 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 it could be confirmed that Boko Haram was involved.
While ransom kidnappings by criminal elements have seen alarming increases in Katsina State, one of this magnitude is unheard of. It recalls the brutal kidnapping of 276 girls from Chibok in 2014 by the Shekau faction. More than 100 of those girls never returned home.
In 2018, a breakaway faction of Boko Haram 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 ordered another such kidnapping.
CNN’s Stephanie Busari and David McKenzie contributed to this report.