PESHAWAR, Pakistan — Pakistani troops clashed with protesters on Sunday near the border with Afghanistan, leaving at least three people dead and scores wounded, officials said.

The violence broke out as several hundred people, including two Parliament members, were protesting for the rights of Pakistan’s Pashtuns in the North Waziristan region. They fought with security officials at a military check post.

A military spokesman described the violence as an assault by members of the Pashtun Tahafuz Movement, or P.T.M., but the protesters disputed that. That movement has galvanized many Pashtuns in recent years with its protests against extrajudicial killings, disappearances and displacements of members of the community in the wake of military operations against the Taliban and other militants.

Most of the Taliban and their leaders, past and present, have been Pashtuns.

Leaders of the Pashtun movement say they are exercising their right to protest peacefully. But the military sees the movement as being propped up by foes of the state and accuses neighboring Afghanistan and India of trying to stir up unrest with support of the movement in areas straddling the Afghan border.