The weak government, already frequently criticized for being subservient to the United States, will likely come under domestic pressure to be tough on the American.
Many Pakistanis regard the U.S. with suspicion or enmity because of its occupation of neighboring Afghanistan and regular missile attacks against militant targets in Pakistan's northwest. The government condemns those attacks, but is widely believed to agree to them privately, further angering its critics.
In a sign of the political sensitivities of the case, Interior Minister Rehman Malik was asked by a lawmaker in parliament whether he was trying to set the American free. "I will never abet a criminal," replied Malik.
A third Pakistani was killed in the incident Thursday in the bustling city of Lahore after being hit by a U.S. vehicle rushing to aid the American, who was also in a car, according to police. Authorities have said the driver could also face charges.
Police officer Umar Saeed said the American, who has not been named by American authorities, had told officers he had withdrawn money from an ATM shortly before the incident, raising the possibility the two men were following him. Others Pakistani officers have said the men were likely robbers, were on a motorbike and both were carrying pistols.
Rana Bakhtiar, deputy prosecutor general for Punjab, said the state would pursue murder charges.
"He has killed two men. A case is registered against him on murder charges," he said.
Bakhtiar spoke after the American appeared in a court in Lahore where judges ordered him to remain in police custody for six days.
The man has been named by Pakistani officials but the U.S. State Department says the name is incorrect.
A top intelligence official in Lahore told CBS News that the man's identity is being investigated. He is believed to work for a private U.S. contractor that provides security at American facilities, the official said.
The U.S. Embassy officially has not said what position the man held at the consulate in Lahore or whether he qualifies for diplomatic immunity from prosecution.
Western diplomats travel with armed guards in many parts of Pakistan because of the risk of militant attack. Lahore has seen frequent terrorist bombings and shootings over the last two years, though the city's small expatriate population has not been directly targeted.
In a two-sentence statement, the U.S. Embassy confirmed that a consulate staffer "was involved in an incident yesterday that regrettably resulted in the loss of life." The U.S. was working with Pakistanis to "determine the facts and work toward a resolution," it said.
In the city of Karachi, around 100 people burned the Stars and Stripes.
"Hang the U.S. spy, the killer of three Pakistanis," read a placard by one of them.
The issue of American diplomats or their security detail carrying weapons inside Pakistan was a hot-button subject last year among certain politicians and sections of the media purportedly worried about the country's sovereignty. They were frequently presented as a threat to ordinary Pakistanis.
"'American Rambo' goes berserk in Lahore,"' read the headline in The Nation, a right-wing newspaper that often publishes anti-U.S. conspiracy theories. Its report described the dead mean as "gentleman" an
Despite the sensitivities of the case, it seems unlikely it will seriously affect ties between the two nations because the relationship is vital for both. Washington needs Pakistan's support to stabilize Afghanistan and defeat al Qaeda, while Islamabad relies heavily on U.S. aid and diplomatic support.
Robbers on motorbikes pulling up alongside cars and holding them up is a common crime in Pakistani cities.
Americans and other foreigners have also been frequently targeted by Islamist militants in Pakistan.
In the northwestern city of Peshawar in 2008, gunmen shot and killed a U.S. aid worker as he drove to work. Suspected militants also opened fire on the vehicle of the top American diplomat in the city the same year, but she survived the attack.