Ramallah Governor Said Abu Ali said the autopsy indicated that Ahmed was struck by a single bullet from an M16 assault rifle that entered his forehead and exited the back of his head.
Israel sought to do a joint autopsy with the Palestinians either in Israel or in the West Bank, but Palestinian officials refused, Ali said.
Residents of Naalin protest almost daily against Israel's separation barrier, and demonstrations frequently turn into confrontations between stone-throwing youths and Israeli troops firing tear gas and rubber-coated bullets.
On Tuesday, Israeli forces started erecting a makeshift fence to prevent protesters from reaching bulldozers clearing land for the barrier. Protesters said troops fired tear gas, rubber bullets and then live fire to disperse demonstrators trying to scale the fence.
The IDF said in a statement that it would investigate the incident. It said its initial inquiry indicated youths were hurling ''rocks in very large quantities.'' The Border Guard said it would deploy forces better trained in riot control to deal with the protests.
Mourners at Moussa's funeral in Naalin. (Photo: AP)
''This type of incident will not repeat itself,'' Superintendent Sharon Manor, a Border Guard company commander, told Israel's Army Radio on Wednesday. Manor said troops did not have permission to use live fire, but did not say whether the IDF thought that was what killed the boy.
Funeral-goers continue struggle
On Wednesday hundreds of people accompanied Moussa's body to its final resting place. Participants cried and prayed over the grave site but vowed to continue the struggle against the separation fence. Slogans cried out included statements such as "Naalin has hammered the final nail into the negotiations' coffin."
Ibrahim Amira, of the Naalin anti-fence committee, told Ynet, "We are determined to continue the struggle, whatever the price may be. We are aware of the fact that nothing can help us but our determination and devotion to the cause."
Amira said the battle against the fence would henceforth be pursued more aggressively. "We will increase the protests and the participants, despite the violence this will draw from the military.
"The army employs serious violence and fires directly towards the demonstrators in order to say – I won't allow you to protest, I will break you. But we won't be broken, we will continue to act with the aim of preventing the construction of the fence and we will dismantle it after it is erected."