Reports of the border clashes emerged hours after suspected anti-government forces on Thursday attacked a police convoy in Karachi, killing at least seven soldiers but missing the city's top military commander.
And a rocket attack in Baluchistan province near the Afghan border left at least a dozen villagers wounded Thursday night.
A Pakistani official, who spoke on condition of anonymity, said the security personnel had been killed in clashes near the mountainous border town of Wana on Wednesday, but the military declined to confirm this.
The military, however, said it had killed more than 20 fighters in intense fighting for a second day on Thursday.
Military spokesman Major General Shaukat Sultan said "some" soldiers had been killed along with three civilians. He said some soldiers had also been wounded but declined to give details.
He said the latest bout of fighting started early on Wednesday when fighters attacked two Pakistan army posts in the Shakai area near Wana.
Security forces responded and surrounded a group of fighters hiding in two or three houses, and another group hiding in mountains, officials said.
"They have scuttled efforts for a peaceful solution and registration of foreigners in the
Major General Shaukat Sultan
Sultan said more than 20 fighters had been killed, while three civilians were killed and three children were wounded in the crossfire.
He said security forces recovered the bodies of six fighters on Wednesday, most of whom appeared to be foreigners. The fighters buried seven of their comrades, he said.
"We have no doubt about the presence of foreign militants in the area," Sultan added. "They have scuttled efforts for a peaceful solution and registration of foreigners in the tribal areas."
More than 120 people, including at least 46 soldiers and 63 fighters, were killed when the Pakistani military launched a failed assault in the area in March.
Early on Thursday, suspected anti-government forces sprayed bullets on a police convoy in the city of Karachi, killing at least seven soldiers but missing their high-profile target.
Three policemen were also killed in the attack on the Karachi corps commander Lieutenant General Ahsan Salim Hayat. Hayat escaped unscathed, chief army spokesman Major General Shaukat Sultan told reporters in the capital Islamabad.
"Seven army men were among 10 people killed in the attack," Sultan later told the private Geo television station.
Hayat is the top military official in Pakistan's largest city of 14 million people, which over the past month has been rocked by anti-government attacks and sectarian unrest that has killed dozens of people.
And on Thursday night, a series of rockets hit three villages near the country's largest natural gas field in southwestern Pakistan, wounding at least 12 people but none of them seriously.
There was no immediate claim of responsibility for the attack But the Sui gas fields and the pipelines taking the gas to other parts of the country have come under frequent rocket attacks this year from disgruntled tribesmen seeking more autonomy.