The health officials suspect the cases to be of the highly transmissible JN.1 variant, which is currently a cause of concern across the world.
The two passengers, between the ages of 50 and 60, arrived from Bangkok and Jeddah on Thursday and Friday, respectively.
The lab samples have been sent to a Dow University of Health Sciences laboratory, they said.
Earlier, the National Command and Operation Center (NCOC) decided to conduct COVID testing of passengers coming from abroad.
The NCOC meeting discussed the situation in the country about the new variant of COVID-19 JN-1. The forum was told that Pakistan has not reported a single case of the new covid variant, so far.
The forum okayed COVID testing at the airports and borders.
Meanwhile, caretaker federal Minister for Health Dr Nadeem Jan said that the government is continuously monitoring the situation as this subvirus of Omicron was found in some countries.
He said that the risk of this variant spreading in Pakistan is very low, but caution is necessary.