Police baton charged Pakistan International Airlines (PIA) employees on Friday, detaining 20 of them, following violent protests as all of the carrier's flights remained grounded for a second day.
Staff have been on picket lines since Tuesday, resulting in the cancellation of around 400 flights, the stranding of 60,000 passengers and causing losses of around ê22 million for the airline, which is on the brink of bankruptcy.
The government's efforts to mediate an end to industrial action have so far failed to resolve the dispute.
"The police baton charged protestors and detained 20 of them after they violently attacked our officials on being asked to clear entry and exit points at the airport," police official Mohsin Ali told AFP.
Local TV footage showed policemen beating the protestors at Karachi airport with batons and putting them into police vehicles.
PIA spokesman Mashhood Tajwar spokesman described the incident as "unfortunate" but added "the continued protest was also affecting businesses of other airlines and the airport itself".
Employees are furious at management plans to farm out lucrative European and US routes to Turkish Airlines in order to avert bankruptcy. They want the plan scrapped and the managing director sacked.
Two rounds of crisis talks between union leaders and government representatives have ended without any breakthrough.
PIA says at least 400 flights have been cancelled since the strike began on Tuesday, including to Britain, the Middle East, Europe and Asia.
"Like yesterday, we have total shutdown today. We had to cancel a total of 370 flights in two days," Tajwar said.
Of the 400 cancelled flights, 325 were domestic and 75 international.
The airline provides the only direct services from Pakistan to Britain, Europe and North America.
Suhail Baluch, president of the Pakistan Airlines Pilots Association, said the strike would continue until the codeshare agreement was abandoned, managing director Aijaz Haroon sacked and all suspended employees reinstated.
Further talks between union leaders and interior minister Rehman Malik were scheduled but no clear timeframe has been given yet.
"We wanted to resolve the issue immediately but the management has violently responded, which can only aggravate the problem," Baluch told AFP.
He said he had got no response from the minister to resume talks.
The PIA spokesman said eight planes were stranded abroad and the airline's other 32 were grounded at different airports around the vast country, where air travel is considered relatively quick and cheap.
"More than 300 Pakistanis are stranded in India with visas about to expire but we cannot carry them back home," he said.
Arch nuclear rivals India and Pakistan on Thursday announced the resumption of peace talks suspended more than two years ago after Islamist gunmen killed 166 people in Mumbai in attacks that India blamed on Pakistani militants.
"Overstaying illegally may put these Pakistanis in danger of being punished by the Indian law," said Tajwar.