Since April, green-shirted members of the People's Party Our Slovakia (LSNS) have been mounting their own "security patrols" aboard trains.
On its website (in Slovak) the LSNS said it had had to act after a 21-year-old woman was "assaulted by a hooligan gypsy [Roma]" on a train near Levice.
Train security is the job of police and rail authorities, the ministry says.
Justice Minister Lucia Zitnanska said nobody could replace the police in protecting citizens. A legal amendment will go before parliament to stop the vigilante patrols.
The LSNS organised patrols on the Zvolen-Levice line, in central Slovakia, alleging that the police were failing in their duty to the public.
The new timetable of the Slovak Railway Company says that nobody can perform activities aboard its trains, unrelated to passenger services, unless they have written authorisation.
In March the LSNS won more than 8% of the vote in Slovakia, entering parliament for the first time, with 14 seats.
Party leader Marian Kotleba is an admirer of Slovakia's wartime existence as a Nazi puppet state, and used to wear a uniform modelled on that state's pro-Nazi militia.
On its website the LSNS says it wants a Slovakia "safe for all decent citizens so they are not terrorised by gypsy or other extremists and corrupted politicians".
It also names pro-Nazi wartime leader Jozef Tiso among "our national heroes". Tiso, a Roman Catholic priest who persecuted Jews in line with Nazi policy, was hanged for treason after World War Two.
Slovakia's justice ministry has drafted a law to stop nationalist vigilantes patrolling trains.