Air traffic around Eindhoven was suspended on Saturday after unidentified drones were reported near the airport, disrupting flights for several hours.
Authorities first noticed the devices late Friday over Volkel air base, where attempts were made to shoot them down but the drones escaped capture.
Following further sightings the next day, officials closed the airspace until about 23:00 local time (22:00 GMT) while security measures were enforced.
Defence Minister Ruben Brekelmans said steps had been taken but gave few operational details.
Volkel is used by the Royal Netherlands Air Force and hosts a US Air Force unit under NATO, raising concerns about the potential risk to military facilities.
Similar overnight drone incursions have been reported at other Dutch bases as well as at installations in Belgium, Denmark and Germany since September, often vanishing before investigators can trace their origin.
Some European officials suspect these episodes could be part of coordinated "hybrid" tactics, a suggestion the Kremlin has rejected.
The lack of concrete evidence has complicated efforts to determine who is responsible.
In response, defence ministers from ten EU countries have agreed to work on a cross-border "drone wall," and several nations are accelerating deployment of anti-drone systems and restrictions, including Denmark's temporary ban on civilian drone flights ahead of a major summit.
