Police broke up a rally in Karachi
They are the first deaths after days of protests against the Pakistan Government's decision to back the United States in its campaign against Afghanistan.
But correspondents say most of the protesters appear to be supporters of religious parties who have called the nationwide strike.
Lynching
Three people were shot dead in Karachi during violent demonstrators in areas dominated by Afghans.
Police used tear gas to break up several rallies as the demonstrators hurled stones and attacked shops and business establishments.
A shopkeeper was lynched to death when he tried to defy the strike call and open his shop.
In Peshawar, which borders Afghanistan, angry protesters gathered before and after Friday prayers to hear religious leaders make speeches in support of the Taleban and Osama Bin Laden.
Pakistani President Pervez Musharraf pledged to co-operate with Washington in trying to capture Bin Laden, who it says was behind last week's attacks in New York and Washington.
Speakers at the rallies attacked US President George W Bush's use of the word "crusade" to describe his planned war on terrorism.
"If America wants a crusade, then we are ready for a holy war," said one preacher.
Cleric warning
In the capital Islamabad, a cleric at the Lal Masjid mosque warned President Musharraf against co-operating with the US.
"Musharraf, listen: The nation will not accept your decision, and any collaboration with the United States is treason," he said.
"The government's hasty decision doesn't enjoy support of the people," said Qazi Hussain Ahmed, chief of the Jamaat-e-Islami, the country's main religious party.
Correspondents say Pakistan is critical to the US campaign and the strike will be an important barometer of public opinion.
Senior Muslim clerics in Afghanistan have called on Bin Laden to leave the country voluntarily.
But they have also passed a resolution calling for a jihad, or holy war, in response to any American attack on Afghanistan, and vowed retaliation against any country supporting US action.
A Peshawar protest organiser told the Associated Press news agency: "If our government gives air or ground space to America, we will declare a jihad against the government."
High alert
In Karachi, some 15,000 police have been put on high alert, concentrating on the airport as well as foreign consulates and businesses.
Police officials said they had received assurances from Muslim leaders that there would be no violence.
A former Pakistani intelligence chief, Hameed Gul, warned that any US attack on Afghanistan would destabilise the entire region.
Pakistan's main political parties, including the Pakistan People's Party and the Muslim League, have however indicated they will support President Musharraf's stance.
Kashmir protest
Meanwhile, police in Indian-administered Kashmir fired teargas on hundreds of Muslims protesting against a possible US attack on Afghanistan.
Security forces also used batons to disperse the demonstrators, who took to the streets of the capital Srinagar to mark a general strike.
The demonstration turned violent after Friday prayers as militants torched US flags outside the city's main mosque.