The Joint Rescue Coordination Centre has set up a crisis centre at the old terminal at Larnaca Airport to coordinate implementation of entry restrictions to Cyprus that came into force at 6 pm on Monday evening.
Transport Ministry permanent secretary Stavros Michail said the aim was to ensure that only those with health certificates are allowed to disembark.
He said that two teams have been set up, one for the airports and one for the ports.
Seventeen flights are expected at Larnaca Airport and eight at Paphos Airport today.
One of the flights has already arrived empty. The second from Qatar had six passengers.
Two Cypriots and an Australian spouse had certificates and disembarked. They are being taken to quarantine. The other three passengers are Nepalese nationals who will be not be allowed to disembark but will return home. Under the new rules, over and above the health certificate entry to Cyprus is allowed only to Cypriots, legal residents and those who work and study here.
According to the Cyprus News Agency 11 of the flights will not have passengers.
All arrivals are subject to 14 days quarantine at government facilities.