The railway station was closed for about two hours on Sunday evening after a sniffer dog barked near a suspicious piece of luggage to alarm the police.
Police closed the station immediately after the alarm and no trains were allowed in. Experts were called in to the scene, who then examined the luggage very carefully and gave all-clear.
"There had been no danger to passengers at any time," according to German federal police.
"The incident had nothing to do with refugees," a police spokesperson reiterated, according to Xinhua.
On the same day, German railway company Deutsche Bahn put in for the first time a regular Intercity-Express train for further transport of refugees. Before Sunday there have only been special trains to transport refugees.
According to Munich police, about 13,000 refugees arrived alone on Saturday at Munich central railway station, so far the only transfer station.
Because of the influx, many refugees were not able to get a bed to sleep when they arrived at Munich on Saturday night. Instead they had to sleep in makeshift tents or on sleeping pads in the reception hall of Munich central railway station.