The boys, aged 10 and 16, were beheaded yesterday in the southern province of Kandahar after they collected left-over food from a police post, provincial police spokesman Ghorzang Afridi told AFP.
"The children used to go to a police checkpoint to collect food and other things thrown away by police, so the Taliban thought they were spies and abducted them and beheaded them," Afridi said.
"They were poor children who lived on collecting scraps and leftovers," he added, saying that villagers found the two boys' bodies in a remote area of Zhari district and informed police.
Speaking to AFP from an undisclosed location, Taliban spokesman Qari Yousuf Ahmadi dismissed the allegations as government propaganda and condemned the murders.
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"The government does this to distract from attacks such as in Kabul this morning," Ahmadi said, referring to a Taliban strike on the capital's airport earlier today.
Seven Taliban insurgents launched a grenade and gun attack on the airport, firing at military buildings before being overwhelmed by Afghan security forces.
No civilians or security forces were killed, but flights were cancelled or delayed for several hours.
Also today, six militants used a truck bomb to attack a provincial council building and voter registration centre in the southern province of Zabul.
All the attackers were killed and three police and 15 civilians were wounded, officials said.