"The Armed Forces can confirm that drones have been observed at several of the Armed Forces' locations during the night. Several capacities were deployed," the military said in a statement.
It provided no other details about the incidents or the military's response.
Danish media reported that no airports had been closed overnight.
Mysterious drone sightings across Denmark and Norway since September 22 have prompted the closure of several airports, with Denmark hinting at possible Russian involvement, charges Moscow has rejected.
On Saturday, Denmark's military said unidentified drones had been observed over "several military sites" overnight Friday to Saturday, but refused to disclose any other details.
Police did confirm that "one to two drones" had been observed on Friday evening near and over the Karup military base, the country's biggest base which houses all of the armed forces' helicopters, airspace surveillance, flight school and support functions.
NATO has "enhanced vigilance" in the Baltic following the intrusions, a spokesperson for the defence alliance said.
The reinforced measures "include multiple intelligence, surveillance and reconnaissance platforms and at least one air-defence frigate" in the region to the west of Russia, alliance spokesman Martin O'Donnell told a press conference overnight Saturday to Sunday.
Copenhagen is to host a European Union summit gathering heads of government on Wednesday and Thursday.
Denmark bans all civilian drone flights this week due to EU summit
Denmark will ban all civilian drone flights across the country this week to ensure security as Copenhagen hosts an EU summit gathering heads of government, the transport ministry said Sunday.
Drones were observed over Danish military sites overnight for the second straight day, Denmark's army said Sunday.
Copenhagen is to host an EU summit on Wednesday and Thursday.
"Denmark will host EU leaders in the coming week, where we will have extra focus on security. Therefore, from Monday to Friday, we will close the Danish airspace to all civilian drone flights," Transport Minister Thomas Danielsen said in a statement.
"In this way, we remove the risk that enemy drones can be confused with legal drones and vice versa," he added.
A violation of the ban can result in a fine or imprisonment for up to two years, the ministry said.
Justice Minister Peter Hummelgaard said in the same statement the purpose of the ban was to simplify the work of police and other authorities.
"The police are on heightened alert, and our authorities must use their forces where necessary to take care of Danes and our guests."
He said the ban would mean police would not have to "spend their efforts on civilian drones" that did not pose a problem to security and police.
Danish police said Saturday they had received more than 500 reports of drone flights from the public, most of which were dismissed as being not of interest.
NATO 'enhances vigilance'
The ban does not apply to military drone flights and state-operated drones, including police and emergency drone operations, as well as health-related drone operations, the transport ministry said.
Neighbouring Norway was also investigating "possible sightings of drones" early Saturday near its biggest military base, Orland, where its F-35 fighter jets are parked.
And Germany said Saturday it wants to authorise its military to shoot down drones after a "swarm" was spotted over the northern state of Schleswig-Holstein, which borders Denmark.
NATO said it had "enhanced vigilance" in the Baltic following the intrusions.
The reinforced measures "include multiple intelligence, surveillance and reconnaissance platforms and at least one air-defence frigate" in the region to the west of Russia, alliance spokesman Martin O'Donnell told reporters.
The string of drone sightings in the past week comes on the heels of drone incursions in Polish and Romanian territory and the violation of Estonian airspace by Russian fighter jets, which raised tensions in light of Russia's ongoing invasion of Ukraine.
Danish investigators have so far failed to identify those responsible for the drone flights over Denmark, but Prime Minister Mette Frederiksen said this week that "there is one main country that poses a threat to Europe's security, and it is Russia."
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