Captain Rifat Haye, who joined Pakistan International Airlines (PIA) in 1990, said in a petition to the court that she had been subjected to "severe intimidation and harassment" by male colleagues since the early years of her career.
Frustrated by the lack of action from her superiors over her complaints, Haye went to the National Assembly's Standing Committee on Women's Development in 2010.
The committee found that two of Haye's superiors had harassed her and other female employees of the beleaguered flag-carrier, Haye's lawyer Jawad Hassan said in his submission.
"Haye also filed cases in high court which ruled in her favour but PIA management did not take any action."
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Chief Justice Tassaduq Hussain Jillani ordered PIA Chairman Muhammad Ali Gardezi to explain within two weeks why no action had been taken on Haye's case.
He also sought comments from the top bureaucrat in the law, justice and human rights ministry about the implementation of the workplace harassment law.
Pakistan passed a law aimed at protecting women from harassment at work in March 2010 and earlier amended its Code of Criminal Procedure to make the offence of harassment punishable by up to three years imprisonment.
The company lost $320 million last year and the deficit would have been much larger if the state had not been pouring money into its coffers in a bid to keep it afloat.
The airline has also been hit by several embarrassing incidents, including the jailing of one of its pilots in Britain in November for being drunk before he was due to fly a plane carrying 156 people.