A district court in Berlin issued the warrant on October 7th, reports Berliner Zeitung.
On August 22nd, 32-year-old Christoph Sch. and his friend Robert S. (37) began racially abusing a woman and her two children on the Berlin S41 ring service.
According to horrified witnesses, the men roared "Heil Hitler" and other Nazi slogans at the family, raising their right arms in Nazi salutes and telling them: "we're the master race."
The 32-year-old then dropped his trousers and exposed his genitals to the children before urinating on them.
Police initially detained the two men, performing breathalyser tests which showed them to be under the influence of alcohol.
The pair were released while the State Office of Criminal Investigations decided whether to investigate the case further – and on October 7th, Tiergarten District Court issued an arrest warrant on the grounds of suspected hate crimes and the use of Nazi symbols.
Police arrested 37-year-old Robert S. at a weekly "Bärgida" demonstration - a Berlin division of Germany's national anti-Islam Pegida movement - according to prosecution spokesperson Martin Steltner.
But a judge spared him custody, as his permanence residence is in Berlin.
"The prosecution appealed against this decision," Steltner said.
Meanwhile, his accomplice Christoph Sch. has evaded arrest.
Police are currently on the hunt for the 32-year-old, Steltner said.
Various politicians have expressed their dismay at the men's alleged crimes.
"People were degraded here – and by abusers who acted like animals themselves," said Frank Henkel, Senator for the Interior.
Berlin mayor Michael Müller also called for a "suitable punishment" for the men.
It's unclear why it took over six weeks from the men's original detainment for a judge to issue an arrest warrant, reports Berliner Zeitung.
Police have yet to trace the woman and her children, who remained on the train after the pair were detained.