Police in Quetta said two members of a banned al Qaeda-linked group had killed themselves with a grenade early Friday after a raid on their hideout.
With tensions remaining high, the commandos were biding their time but would be sent out "on an urgent basis to deal with any situation," said Lieutenant General Safdar Hussain, army commander in NWFP.
The commando force demonstrated its skills at a dress rehearsal in Multan on Thursday, in which pretend militants attacked a mock Shia procession and staged a chase with military helicopters and ground forces.
"We wanted to assess the ability of the force and test the security arrangements," the force's commander Brigadier Mohammad Ibrahim told reporters.
The commandos were being deployed in parts of Punjab and in NWFP on the Afghan border.
Tens of thousands of police and paramilitary forces were covering the rest of the country, officials said, including 4,000 in Islamabad and 15,000 in Karachi.
Authorities in Punjab have declared about a dozen places, including Jhang, Multan, Faisalabad and Bahawalpur as sensitive areas.
"Miscreants trying to disturb peace will be crushed with an iron hand," military commander of Faisalabad, Lieutenant General Javed Alam Khan said.