The first balls were installed just above carriage-height near a station outside the capital, Jakarta.
More will be put up elsewhere if they are a success.
Previous attempts to deter roof riders included spraying them with paint, spreading oil on carriages and hiring musicians to perform safety songs.
Correspondents say those initiatives have failed. Officials hope that the latest move will prove to be the ultimate deterrent.
The balls – which can deliver a severe blow to the head – will be suspended a few inches above the tops of carriages at points where trains enter or pull out of stations, or where they go through crossings.
Critics say that ‘roof surfing’ takes places because there are not enough trains
Officials told the BBC that “roof surfing” can be extremely dangerous. In 2008 at least 53 passengers died in an accident after boarding a train roof. In 2011, 11 people were killed.
Critics say that the problem of “roof surfing” will never be completely ironed out until there are fewer delays and enough trains to meet demand