Aviation Division spokesman Abdul Sattar Khokhar said, Civil Aviation Authority (CAA) imposed a fine of Rs100,000 on the Qatar Airways.
Government had taken serious notice of the violation that put the health and safety of the passengers as well as personnel working at the airport at risk.
The airline shall also be responsible for all expenses incurred on the testing of Covid-19 and quarantine of the passengers and the staff, he said.
He said one of the passengers with a positive Covid-19 test report had travelled on the Qatar Airways flight to Islamabad.
The CAA has already directed the airlines operating flights to and from Pakistan to ensure compliance with the SOPs that have been devised and implemented to protect passengers from contracting the virus.
Meanwhile, Aviation Minister Ghulam Sarwar Khan chaired a meeting regarding outsourcing of major airports, aviation division, the spokesman said.
Mr Khan was informed that as per directions of the cabinet, an audit firm shall be hired in the initial phase to carry forward the process in accordance with the best international practices.
The minister for privatisation, adviser to the prime minister for institutional reforms and austerity, the Board of Investment chairman and aviation secretary were also present in the meeting.