In a letter served to SAI on Monday, the CAA directed the airline to inform the passengers affected to avoid any inconvenience to them.
SAI is a defaulter of more than Rs1.25 billion of CAA with regard to various charges, according to the authority.
The CAA asked the passengers in the affected flights to make alternative arrangements.
Shaheen Air cuts fleet by six aircraft as skies become loaded
On a separate note, the airlines has also decided to reduce its fleet, putting up six of its aircraft on sublease to the Royal Jordanian Airline.
The development highlights issues faced by domestic carriers that are struggling to match wits with foreign airlines in an open-skies framework.
Industry experts believe Pakistan's aviation industry is already saturated with several players vying for domestic and international travel space.
SAI's decision to reduce its fleet also comes on the heels of a tax controversy where it failed to pay the Federal Board of Revenue (FBR) on time. The tax body sealed the airline's head office before the dues amounting to Rs910 million were paid.
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