Pakistan International Airlines (PIA) said it is investigating how seven extra passengers were allowed to stand in the aisles on a flight to Saudi Arabia.
The passengers were allowed on the 20 January flight to Medina despite every seat being filled, the airline said.
Details of the flight have only emerged now because of extensive investigations by Dawn newspaper.
Staff had issued additional handwritten boarding passes, the paper reported.
Such an over-crowded flight would have caused problems in an emergency evacuation, aviation experts said, and passengers would not have had access to oxygen if it was suddenly required.
The flight in question went from Karachi to Medina carrying a total of 416 passengers, on a Boeing 777 with a total seating capacity of 409, including staff seats, the BBC reporter.
Anwer Adil, the flight captain, said he found out about the extra passengers only after take-off. Adil said he could not turn back to Karachi as it would have meant dumping fuel, which was not in the interest of the airline