Aalborg airport in the country's north was forced to shut down for several hours after green lights were spotted overhead. Three smaller airports in the south also reported drone activity.
On Monday Copenhagen airport temporarily closed due to a drone incursion.
Defence Minister Troels Lund Poulsen told a news conference that the "hybrid attack" was part of a "systematic operation", but said the devices had been launched locally.
A hybrid attack uses a mix of military and non-military tactics and is designed to interfere with a nation's infrastructure or institutions.
Comment: The Danish war minister appears to be simply guessing without any evidence and likely in an attempt to distract from the possibility of an incursion from another realm.
Drones pose a risk of colliding with planes, particularly during take-off or landing, but halting air traffic in and out of an airport to avoid this can cause delays and flights being redirected elsewhere.
At least three flights were diverted away from Aalborg during the incident.
Poulsen added that there was no evidence to suggest Russia was behind the incursion. Danish police are now seeking to find out who launched them.
Russia has been accused of conducting hybrid attacks in the past, and Europe has been on high alert after several Nato member states reported Russian incursions in their airspaces.
Estonia and Poland requested a consultation with other Nato members last week, after around 20 Russian drones crossed into Poland and Russian MiG31 jets entered Estonian airspace in a separate incident. Romania, another Nato member, also said a Russian drone had breached its airspace.
Russia denied violating Estonia's airspace, while it insisted the Polish incursion was not deliberate. It did not comment on the incident in Romania.
Suspicious drones have also been sighted over Germany and Sweden. All are suspected - but not proven - to be part of Russia's indirect aggression towards Nato states supporting Ukraine.
Danish Prime Minister Mette Frederiksen said Russian involvement in the Copenhagen drone incursion could not be ruled out, describing it as "the most severe attack on Danish infrastructure so far". The incident also saw Oslo airport in Norway temporarily close.
Comment: The Danes are blowing hot air to fuel the Russophobia. To be fair, hot air is about all which Denmark has left as it has sent most of its military equipment to Ukraine.
Kremlin spokesman Dmitry Peskov called the allegations "unfounded".
Officials said the Danish Armed Forces had been affected by Wednesday's incident, as Aalborg airport is also used as a military base.
The drones were not shot down, despite Danish authorities saying they had the ability. Officials said this was due to concerns for the safety of the surrounding population.
Comment: Yeah, really. Whatever you say.
"If we get the opportunity, we will take down the drones," chief inspector Jesper Bøjgaard Madsen said.
Comment: That is confusing. Does that mean that the opportunity wasn't there before and that the UAVs could be in the Danish airspace for 2-3 hours without an 'opportunity'. Given that the 'drones' had lights on it should have been easy to follow them. And yet it is not known from where they arrived and where they suddendly disappeared to. No functioning radars?
Police said they did not believe there was any danger to passengers at the airport or residents, but asked the public to keep their distance from the area.
Peter Hummelgaard, Denmark's justice minister, said the hybrid threats were "here to stay".
Poelsen noted that an EU meeting had been called for Friday, at which enhanced drone preparedness across Europe would be discussed.
Earlier this month, European Commission President Ursula von der Leyen called for a "drone wall" to tackle incursions launched by Russia.
What that means is not entirely clear - but detecting the drones early and then destroying them are seen as key elements of such a strategy.
US President Donald Trump has gone as far as to say that Nato nations should shoot down Russian planes in their airspace, while Nato has warned it would use "all necessary military and non-military tools" to defend itself following the recent military incursions.
"We are a defensive alliance, yes, but we are not naive, so we see what is happening," Nato's secretary general Mark Rutte said.
Comment: Two lies in one sentence. The Nato secretary general is outdoing himself. It is not a defensive alliance and yes, they are naive!
The claim that these are drones, makes a mockery of the Danish defence with radars not detecting where they came from or where they disappeared to, the F-16 and F-35 jets not able to either take them down or intercept them over a period of several hours.
See also this article about the incident which happened 48 hours earlier: They're back! Several large 'drones' fly over Copenhagen and Oslo airports, shutting down civilian flights, before 'disappearing'