The situation at the station during Oktoberfest which begins in two weeks will already be testing for police, Bavarian interior minister Joachim Hermann told the Münchner Merkur on Friday.
If refugees arrive in the numbers seen on Tuesday the station would get very crowded, he added.
Munich station is the main arrival point for refugees currently travelling to Germany via Hungary. On Tuesday alone an estimated 1,500 asylum seekers arrived at the station.
There were reports in Hungarian media on Friday of clashes between refugees and a mob of football hooligans in Budapest's Keleti station, and Munich authorities will be hoping to avoid a repeat.
"It's also impossible to predict how some drunken Oktoberfest visitors will behave,“ Hermann said, pointing out that every year during the beer festival there are incidences of violence at Munich's main transport hub.
The Christian Social Union (CSU) politician told the paper he had demanded from federal interior minister Thomas de Maizière that he strengthen the Bavarian police with reinforcements from other German states.
"The minister promised me the he would make it a priority,“ said Hermann, although he could not yet say how many more officers would be supplied to the Bavarian capital.
Thomas Baumann, spokesperson for the Munich police, said that they would "find a solution to ensure that the masses of people are channeled through correctly."
During Oktoberfest the police's current policy of meeting refugees on the station platform and accompanying them to a wing of the station called the Starnberg wing will continue, minimizing contact between refugees and party-goers, reports the Münchner Merkur.
Violence has long been recognized as an unwanted side effect of the high levels of alcohol consumption which happen at Oktoberfest.
In 2014 police reported a drop in crime on previous years. But 16 cases of grievous bodily harm were reported, while a British man was one of two people raped during the sixteen-day event.