Wizz Air said in a statement it would lay on extra flights from the Romanian city of Iasi as replacements, including a new service to Berlin, and more flights to Barcelona, Milan Bergamo, Bologna, Rome Ciampino, Rome Fuimicino, Dortumand, Larnaca, London Luton and Treviso.
Flights to Budapest and Prague will not be replaced and those inbound to Chisinau will be reallocated to other destinations in the Wizz Air network, it said.
Tensions between Russia and Moldova have grown in recent months as Russian missiles aimed at Ukraine have entered Moldovan airspace and authorities have blamed the Kremlin for fuelling anti-government protests, something it denies.
It said the civil aviation authority and the ministry of infrastructure and regional development had been in "constant cooperation" with Wizz Air representatives and informed them of the procedures in place to ensure aviation security.
The aviation authority would take "all necessary actions" to return Wizz Air to Chisinau airport as soon as possible, and to attract other low-cost airlines.