The Bundeswehr base in Cologne-Wahn was locked down because of "a suspicion of an attempted intrusion and a suspicion of sabotage," defence ministry spokesman Colonel Arne Collatz told reporters in Berlin.
A hole was discovered in a fence near drinking water storage facilities, the military's territorial command said on X.
The perpetrators had not been found and the site's water was being checked as a precaution. The base re-opened later in the day, it added.
Der Spiegel magazine reported that soldiers and civilians on the Bundeswehr base had been advised not to drink the tap water over concerns that the water supply "may be contaminated".
The Cologne-Wahn base, located near Cologne-Bonn airport, houses several military and civilian facilities of the German armed forces as well as aircraft used by Chancellor Olaf Scholz and his ministers for government travel.
The base is also an important hub for military support for Ukraine. Ukrainian soldiers regularly fly home from there, via Poland, after receiving training in Germany, Der Spiegel added.
- Security stepped up -
A NATO base in the western German town of Geilenkirchen meanwhile faced an attempted trespassing incident late Tuesday, the military alliance said in a statement.
An individual attempted to enter the base but was stopped and sent away, a spokesman said, adding that a "routine" sweep of the site and people there was conducted afterwards. Police are investigating the incident.
Following the lockdown at the Cologne-Wahn base, the NATO site also increased its security level and conducted routine checks of its water supply but added it had no concerns with the safety of its supply.
The base, home to NATO AWACS reconnaissance aircraft, was not sealed off and continued operating at full capacity, the spokesman said.
Defence Minister Boris Pistorius told Der Spiegel that the authorities "reacted quickly" at both sites by sealing off access, alerting investigators and ordering laboratory analyses to check for possible contamination.
"These incidents show we must remain vigilant," he added.
Marcus Faber, a German lawmaker from the liberal FDP party and chairman of parliament's defence committee, told Bild daily that with the two incidents coming so close together "one can assume that an enemy actor wants to demonstrate his sabotage skills".
Germany -- a key ally of Kyiv -- has been on high alert for sabotage and attacks on military facilities in the country in the wake of Moscow's 2022 invasion of Ukraine.
In April, investigators arrested two German-Russian men on suspicion of spying for Russia and planning attacks in Germany -- including on US army facilities -- to undermine military support for Ukraine.
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