Pakistani officials accused up to 60 Afghan soldiers on Monday of crossing into Pakistani territory and sparking clashes that killed two tribesmen.
It was the latest in a series of escalating cross-border attacks reported in Afghanistan and Pakistan that are inflaming tensions along the porous border as NATO prepares to end its combat mission against the Taliban in 2014.
Both countries blame each other for Taliban fighters active on both sides of their 2,400 kilometer border, fanning distrust between Kabul and Islamabad, and complicating a peace process in Afghanistan.
Kabul threatened to report Islamabad to the UN Security Council over what it alleges is the shelling of villages, while Islamabad said it would protest formally to Kabul against the latest incursion.
In Pakistan's semi-autonomous tribal belt, security officials said two tribesmen were killed in Upper Kurram district in clashes with 60 Afghan army soldiers.
Another tribesman was also wounded "after they traded fire with Afghan army soldiers on seeing them inside Pakistani territory," a senior official said.
The clashes lasted for more than 90 minutes after which security forces were sent to the area on the Afghan border.
Afghan defense officials denied the alleged incursion.
"We are not aware of such an operation by ANA (Afghan National Army) in that area," Daulat Wazir spokesman for the Ministry of Defense said.
Colonel Ahmad Jan, spokesman for army corps 203 in southeastern Afghanistan said: "It is not true, our forces have not entered Pakistan. We have not had any operations near the border recently."
A spokesman for Afghanistan's National Directorate of Security intelligence agency said cross-border fire had killed four people, including a woman and a child, and wounded six others, in the last week.
Afghans and Americans blame Pakistan for not doing more to eliminate havens on its soil, which are used as launch pads for attacks across the border.
Last month, the US commander of NATO in Afghanistan blamed the Pakistan-based Haqqani network for a siege on a lakeside hotel in Kabul that killed 18 people.
Officials said dozens of militants based in Afghanistan on Sunday attacked a checkpost in Upper Dir, a district in the government-controlled part of Pakistan.
They said six militants were killed after crossing into Sabir Killey village in the Soni Darr area of Upper Dir.