"The peace and reconciliation programme initiated by the Afghan government is a good opportunity for the Afghan armed opposition, specially their commanders, to stop the destruction (of Afghanistan)," said Khalili.
"Otherwise eventually they will face the same fate as Osama bin Laden," he added.
Khalili reiterated that bin Laden's killing in Pakistan showed that Afghan claims were correct that al Qaeda and Taliban leaders enjoyed support from elements in Pakistan.
"The killing of Osama bin Laden, the leader of al Qaeda, gives us hope that the voice of the people of Afghanistan is now being heard," he said.
President Hamid Karzai inaugurated a High Peace Council charged with negotiating with the Taliban last year but the process has so far shown few public signs of progress.
The two-day conference features Afghan cabinet members, ambassadors, Afghan provincial governors plus representatives of the United Nations.
Taliban spokesmen have ruled out peace talks unless foreign forces leave Afghanistan but it is not clear if they speak for all Taliban.
The militia is waging a nearly 10-year war against US-led foreign forces in Afghanistan, which currently number around 130,000, plus the Afghan police and military.