Baloch militants have targeted railway tracks, power facilities and other key installations in a campaign which has run for two years.
As their campaign continues, Pakistan's human rights commission has detailed widespread violations by the security forces, including extra-judicial killings - a report government officials say is one-sided.
Balochistan has a long history of resisting external influences
No-one seems to know exactly how many civilians have died in helicopter raids on suspected militant camps or in the numerous rocket attacks on soldiers' camps.
In the words of one analyst, it's an undeclared war in which neither side is observing the rules.
So what on earth is going on in Balochistan, which is regarded as the poorest and most backward of Pakistan's four provinces?
With about six million inhabitants, Pakistan's biggest province has less than half the population of the port city of Karachi.
In mineral resources, however, it is said to be the richest province and is a major supplier of natural gas to the country.
With the government now planning to construct a deep sea port at Gwadar and a road link with Afghanistan and central Asia, Balochistan has acquired a new significance - both for Pakistan and other regional players.
And that is where the problem lies.
For decades, Baloch nationalists have been critical of the central government in Islamabad, accusing it of depriving the province its due.
They say the government took away income from natural gas and other resources, while spending only a trivial amount on the province.
Octogenarian warrior Nawab Akbar Bugti, reported killed by Pakistan in August 2006, mixed 17th century guerrilla tactics with modern weaponry to take on the might of Pakistan's security forces.
No-one knows exactly how many have died in the violence
Near the mountain hideout of his Bugti tribe, another chieftain, Nawab Khair Baksh, has been fighting a similar battle with security forces in the district of Kohlu.
The struggle for greater national rights, financial resources and against the establishment of military camps in Balochistan led to a tacit understanding between Nawab Bugti and Nawab Baksh.
One of Mr Baksh's six sons leads a force of trained and semi-trained Marri tribesmen, which goes by the name of the Balochistan Liberation Army (BLA).
A third tribal leader, former Chief Minister Ataullah Mengal, is not involved in the armed struggle but gives it his ideological and political backing.
For these nationalist leaders, large projects such as the highway and Gwadar port scheme are another form of subjugation - serving the central government but offering little benefit to Balochistan.
The military garrisons set up in the area to secure the expected foreign investment are, for the rebels, also part of well-conceived plan to suppress the nationalist voice.
President Musharraf refers to these tribal chiefs as anti-development.
He says they oppose his projects because they will bring prosperity to the area and will end the archaic tribal system which preserves their power.
Without naming any country, he also accuses the armed Baloch militants of playing into foreign hands.
Senior officials in the security forces say they grew alarmed when intelligence agencies found more than one foreign country was involved in the province's affairs.
The countries were said to be opposed to Gwadar becoming a major trading port for central Asian nations and China.
One official said the biggest shock came when the interrogation of a group of militants revealed they had been trained in a friendly Gulf country, which allegedly feared it could lose its status as the region's biggest trading port.
But no matter what the authorities say about foreign involvement, seasoned Balochistan watchers say the problem is essentially local.
They say the Baloch people can only be tamed through political means, pointing out that this is not the first time they have taken up arms to fight those they see as outsiders.
And, they say, though the might of the armed forces might crush the people of Balochistan, it will never win their hearts and minds.