The Bundespolizei, which police the country’s transport network, said they had stopped 600 illegal immigrants at Munich’s central station since June.
“For months we've seen a huge increase at Munich Hauptbahnhof of unauthorized people entering the country," officers said on Tuesday.
Most are refugees arriving from war-torn Syria and Eritrea in Africa.
Among the 49 found on the train from Verona on Monday night, 35 were Syrians, including four large families and 14 children. There were also people from Somalia, Nigeria, Gambia and Eritrea.
Police said they established the identity of those on board and then handed them over to the Bavarian Ministry for Migration and Refugees.
And on Tuesday, officers in Bavaria arrested three Italians on the A93 motorway near Rosenheim who were allegedly illegally transporting 25 Syrians in three vehicles into Germany.
Four children were among the passengers, who had been smuggled across the Mediterranean and then on to Milan. Each had paid several hundred euros to be brought from northern Italy towards Munich, police said.
They were sent to a centre for refugees.
The drivers, meanwhile, aged 71, 51 and 49, are being investigated for people smuggling, police said on Wednesday.