As per the complaint lodged by their mother Sunderbai yesterday, Nilesh (12) and Ganpat (7) went missing from their house in Kothali village in the district on May 17, a senior police official said.
The complaint was lodged at Muktainagar police station, he said.
"We have taken the matter seriously and as per the Supreme Court's guidelines, we registered an offence of kidnapping against unidentified persons," the official added.
According to him, five special police teams have been formed to trace the duo.
On August 30, 2014, Nilesh had saved a minor boy Bhagwat Ghogale, who had accidentally slipped in an artificial pond in front of a local temple.
For the act, Nilesh had received the award from Prime Minister Narendra Modi on January 26 this year.