The clashes at Ladha fort on Friday erupted after fighters started firing rockets and small arms at the outpost in the morning, after which dozens of attackers started to gather around the building.
"Security forces used artillery, mortars and small-arms fire to engage the miscreants. Reportedly, 50-60 miscreants were killed and [the] rest of them dispersed," the army said in its statement.
Taliban and al-Qaeda fighters are said to be sheltering in Pakistan's tribal regions.
The growing unrest in Pakistan's tribal area has underlined US fears that Pakistan, a key ally in the US's so-called "war on terror", is spiraling out of control.
Michael Hayden, the CIA director, said in an interview published in the Washington Post on Friday that the CIA believes Baitullah Mehsud, a tribal leader with links to al-Qaeda, was behind the assasination of Benazir Bhutto, the opposition leader killed in December.
Hayden said the assasination "was done by that network around Baitullah Mehsud. We have no reason to question that".
The latest fighting in Waziristan came two days after hundreds of heavily armed militants overran another Pakistani paramilitary fort in South Waziristan.
Seven soldiers were killed in that attack and another 15 troops are missing, presumed kidnapped.