The chain of fires began during the morning rush hour at the suburban Haedo station, 16 kilometers (10 miles) west of Buenos Aires, and quickly spread to the neighboring Ramos Mejia and Ciudadela stations.
Commuters reacted angrily after service was suspended following a derailment near a station in the city.
But Justice Minister Juan Pablo Schiavi said the privately owned operator, Trenes de Buenos Aires, had lodged a complaint of "sabotage."
"The near-simultaneous nature of the fires was striking and the fact that security cameras were damaged at all three stations makes one think it was something organized and intentional," said a spokesman for Trenes de Buenos Aires, Gustavo Gago.
Witnesses said youths sacked a ticket office in Haedo, while railroad workers said they were set upon by furious passengers.