"Security forces returned the fire and are in the process of clearing the miscreants' training facility," the military said in a statement on Tuesday.
Pakistan's tribal areas on the Afghan border are hotbeds of many foreign al-Qaeda members who took refuge there after US-led forces ousted the Taliban in Afghanistan in 2001.
Beginning in 2003, Pakistani security forces launched offensives in North and South Waziristan as part of efforts in the US-led "war against terror".
A senior US official said on Monday that Pakistan had been increasingly active in repelling Taliban and al-Qaeda forces on the Afghan border despite growing unease about Pakistan's commitment to the war on terrorism.
In February, Dick Cheney, the US vice-president, visited Afghanistan and Pakistan and urged Pervez Musharraf, the Pakistani president, to take tougher action against armed groups on his side of the lawless border where US commanders say radical fighters are training.