Tribal fighters fired rockets at the Razmak Camp in north Waziristan, killing one solider and wounding two, the military said in a statement.
The soldiers responded with artillery and mortar fire, but there was no detail on any casualties.
In southern Waziristan, Pakistani troops attacked fighter hideouts and reinforced outposts.
Major General Athar Abbasm, a military spokesman, said: "Troops are engaging miscreants and attacking their hideouts."
"We are reinforcing the [military] posts in south Waziristan because of the continued attacks from miscreants."
The violence in the border region, as well as a series of suicide attacks that have killed hundreds in recent months, is triggering uncertainty in Pakistan ahead of February 18 elections that many predict will weaken Musharraf's grip on power.
Musharraf, who is touring Europe seeking support for his embattled government, rejected claims that the violence was a sign of a resurgent Taliban.
He said: "These are pinpricks that they keep doing - and we have to manage all of that."
Musharraf said "it doesn't mean much" that Osama bin Laden and Ayman al-Zawahri are still at large, and that 100,000 Pakistani troops deployed to the region are not focused on locating the two, believed by many to be in the border region.
North and south Waziristan emerged as a front line in the so-called "war on terror" after Pakistan allied itself with the US following the September 11 attacks.
Washington has given Pakistan billions of dollars in aid to help government forces battle pro-Taliban fighters.