The train is reported to have slammed into the barrier at the end of the platform at the Once station in the west of the city.
The injured driver and some passengers were taken away on stretchers, with the first carriage the worst affected.
The ministry of transport said it could not rule out fatalities, with many people still said to be trapped.
One of the carriages was driven nearly six metres (20ft) into the next, he said.
“There are people still trapped, people alive, and there may have been fatalities. We don’t know if there are dead people in the wreckage,” JP Schiavi said.
Survivors told the TeleNoticias channel that many people had been injured in a jumble of metal and glass.
In September 2011 eleven people died when another commuter train in Buenos Aires hit a bus crossing the tracks and then hit a second train coming into a station.
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