Two employees of Pakistan International Airlines were killed after a standoff with police on Tuesday, which led the national flag carrier to wind down its operations across the country.
As news of the deaths spread on Tuesday evening, the flight operations began shutting down in solidarity with the protesters, officials said.
The operations were suspended around 4 pm at Lahore, Islamabad, Peshawar and Quetta airports, officials confirmed.
PIA Lahore spokesman Athar Awan said flight operations were halted after two PIA employees were killed in clashes with police and Pakistan Rangers.
A Civil Aviation Authority official in Quetta, on condition of anonymity, told Dawn that flights to and from Quetta were delayed indefinitely following the protest outside Karachi airport.
Two protesters died after they sustained bullet injuries and five others were injured, but Rangers and police denied "handling protestors violently" and opening fire on them at the site of the clash, Dawn reported.
The incident came a day after Prime Minister Nawaz Sharif enforced the Essential Services Maintenance Act, 1952, for six months in an effort to block the impending strike of the airline staff.
The employees of Pakistan International Airlines are opposing the airlines' privatisation and are determined to disrupt flight operations from Tuesday despite the government's threat to terminate their services for work stoppage.
A large contingent of Rangers and police personnel was stationed outside the major airports to control the protestors and avoid any violence.
Police and paramilitary rangers deployed tear gas and water cannon against the protesters from Pakistan International Airlines after they blocked the main entrance to Karachi's Jinnah International Airport around midday.
Gunfire later erupted, although the source of the shots was unclear. Both law enforcement agencies denied they had shot at protesters.
Dr Seemi Jamali, a spokeswoman for the government-run Jinnah Postgraduate Medical Center, told AFP the hospital had received a total of 10 wounded, one of whom later died.
"Four people with gunshot wounds were brought to the hospital, one succumbed to his injuries while the other three are in stable condition," she said. Six others, among them journalists who had been covering the protest, were treated for other injuries.
Another employee, who had also been shot, was taken to the private Aga Khan University Hospital, where he was pronounced dead on arrival.
"The PIA employee was brought dead to our emergency department and our team attempted to revive him for 20 minutes," a spokesman of the hospital told AFP, identifying the deceased as Inayat Raza.
Nadeem Jaffer, a colleague and friend of Raza, confirmed his death at the hospital.
Kamran Fazal, the police chief of the city's eastern district said: "The situation escalated when a couple of gunshots were fired. My officers told me that they might be fired from the crowd.
"We are searching for the empty shells and only then can we establish who opened fire."
The PIA employees' union had announced a day earlier its plans to shut down the airline's flights after weeks of token strikes against government proposals to complete the partial sale of the carrier by July.
The move follows years of crushing losses and mismanagement that have battered the airline's reputation.
PIA suffers from frequent cancellations and delays and has been involved in numerous controversies over the years, including the jailing of a drunk pilot in Britain in 2013.
The airline has also traditionally handed out tens of thousands of free tickets each year, contributing to its losses.
With agency inputs