According to local media, the boys were beheaded in Afghan province of Kandahar on charge of spying.
One of the boys, a 10-year-old, is reported to have regularly accepted food handouts from police in the Zhari district to feed his family.
His killing is said to have taken place on Sunday but news only emerged on Monday as the provincial government condemned it and asked the public to report suspicious behavior and people.
Later on Monday Kandahar's provincial government posted an update saying that a 16-year-old had also been beheaded by the Taliban.
Kandahar's governor condemned the beheading as inhumane and un-Islamic.
Little is known about the other boy, who was 16 years old.
But Taliban spokesman Qari Yousef Ahmadi insisted to the BBC that the group had not beheaded any children in the area.
In 2012 the Taliban were accused of beheading a 12-year-old boy and a seven-year-old girl in south and east Afghanistan - the group denied responsibility in both those cases.