At a meeting with Afghan religious leaders, Karzai said some clerics in religious schools in neighbouring Pakistan were teaching young Afghan refugees that they had a duty to fight a jihad against his government.
"When a young Afghan, whose intention of entering the religious school is to learn about the Quran and religion, gets sent back to his country to kill the road workers, it spells disaster for Afghanistan, whether or not he succeeds in his ominous mission," the Afghan interim leader said.
Karzai's appeal came against the backdrop of shrill Afghan accusations that Pakistan was not doing enough to nab members of the Taliban, who sought safe havens across the borders.
The president urged Afghan clerics to intensify their dialogue with Pakistani clerics. But he said only a few Pakistani clerics were part of the problem.
"(There are) those who are few in numbers and who pretend to be running the madrassas for the study of religion, but who in reality train militants for Afghanistan," Karzai said.
"I want our ulema and the ulema of Pakistan to sit together and consider the problem of those elements that are damaging religion under the banner of religion," he said.
Karzai's appeal to the clerics reflected growing concerns within the Afghan government over spiraling violence, which is mostly blamed on the resurgent Taliban.
Despite being driven out by the US-led troops in late 2001, the Taliban is believed to be rapidly regrouping. Afghanistan blames Pakistan for allowing Taliban fighters to sneak into the country across the borders.