Three hijackers boarded the train from a station in West Java and forced the locomotive driver to divert the train, a transport ministry spokesman told Xinhua.
Police nabbed two hijackers while one escaped when the train stopped at the Senen station in Jakarta. The incident triggered panic among the people as police fired a few gunshots, the spokesman said.
About 16 million people in the Muslim-dominated country are expected to travel home by trains during the festive season, he added.